- AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
-
The filter string used for sites that fail the allele balance filter.
- AbstractAlignmentMerger - Class in picard.sam
-
Abstract class that coordinates the general task of taking in a set of alignment information,
possibly in SAM format, possibly in other formats, and merging that with the set of all reads
for which alignment was attempted, stored in an unmapped SAM file.
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
-
Constructor
- AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
-
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed
x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary
x-y float pairs.
- AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Use this ctor if lane and tile are not discernible from file name.
- AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
-
- AbstractInputParser - Class in picard.util
-
Class for parsing text files where each line consists of fields separated by whitespace.
- AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
-
- AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that perform duplicate
detection and/or marking within SAM/BAM files.
- AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
-
Little class used to package up a header and an iterable/iterator.
- AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
- AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
-
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to accept SAMRecords one at a time.
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
-
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
-
- acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
-
- acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Adds information about an individual SAMRecord to the statistics.
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
-
- acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
-
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
-
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass
this value to all collectors that should include this record
- acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
-
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
- accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
-
Incorporates the provided variant's data into the metric analysis.
- accumulate(VariantContext) - Method in class picard.vcf.GvcfMetricAccumulator
-
- accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
-
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
-
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
-
- accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
- accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
-
- ACCURACY - Variable in class picard.sam.DownsampleSam
-
- ACTION - Variable in class picard.util.IntervalListTools
-
- ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
-
- ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
-
- AdapterMarker - Class in picard.util
-
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
- AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
-
Truncates adapters to DEFAULT_ADAPTER_LENGTH
- AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
-
- AdapterPair - Interface in picard.util
-
- ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
-
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
-
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
- adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
-
- adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with default parameters for a single read.
- adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
- AdapterUtility - Class in picard.analysis
-
A utility class for matching reads to adapters.
- AdapterUtility(List<String>) - Constructor for class picard.analysis.AdapterUtility
-
- add(HaplotypeProbabilities) - Method in class picard.fingerprint.Fingerprint
-
- add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
-
Adds a trio to the PedFile keyed by the individual id.
- add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Add a record to the mark queue.
- add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Adds the end to this set, if not already added based on physical location
- ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
-
- ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
-
- addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
-
Add all metrics to the given file in the following MetricAccumulationLevel order
ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
- addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Adds a single point of depth at the desired offset into the coverage array.
- addBaseQHistogram(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- AddCommentsToBam - Class in picard.sam
-
A tool to add comments to a BAM file header.
- AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
-
- addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
-
- addExon(int, int) - Method in class picard.annotation.Gene.Transcript
-
- addHaplotype(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeMap
-
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
- addInfo(SamLocusIterator.LocusInfo, ReferenceSequence) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
-
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
-
- addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.ReadNameParser
-
Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it
can be used later to determine optical duplication
- addLocusResult(LocusResult) - Method in class picard.fingerprint.MatchResults
-
- addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- addMetricsToFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
-
- addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
- addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
-
- addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
-
Any metrics collected will be added to the metric file provided.
- addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) - Static method in class picard.vcf.GenotypeConcordance
-
Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
- AddOrReplaceReadGroups - Class in picard.sam
-
Replaces read groups in a BAM file
- AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
-
- addResults(MatchResults) - Method in class picard.fingerprint.FingerprintResults
-
- addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Adds a row to the scheme
- addSnp(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Adds a SNP to the haplotype.
- addToLogLikelihoods(Snp, List<Allele>, double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Adds a base observation with the observed quality to the evidence for this haplotype
based on the fact that the SNP is part of the haplotype.
- addToMetricsFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- addToMetricsFile(MetricsFile<CollectWgsMetrics.WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
-
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype
based on the fact that the SNP is part of the haplotype.
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype
based on the fact that the SNP is part of the haplotype.
- addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
-
- advance() - Method in class picard.util.AbstractInputParser
-
- advanceFile() - Method in class picard.util.BasicInputParser
-
- ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
-
- ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of aligned reads used to compute the gc bias metrics.
- ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
-
- ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
-
- ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
-
- ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
-
- ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
-
- ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
-
- AlignmentSummaryMetrics - Class in picard.analysis
-
High level metrics about the alignment of reads within a SAM file, produced by
the CollectAlignmentSummaryMetrics program and usually stored in a file with
the extension ".alignment_summary_metrics".
- AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
-
- AlignmentSummaryMetrics.Category - Enum in picard.analysis
-
- AlignmentSummaryMetricsCollector - Class in picard.analysis
-
- AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
-
- ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
- AlleleBalanceFilter - Class in picard.vcf.filter
-
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
- AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
-
- ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
-
- ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
-
- ALLOW_DUPLICATE_READS - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
-
- ALLOW_MISSING_FIELDS_IN_HEADER - Variable in class picard.vcf.LiftoverVcf
-
- ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
-
- Alpha - Class in picard.cmdline.programgroups
-
- Alpha() - Constructor for class picard.cmdline.programgroups.Alpha
-
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls
at G reference bases that are correlated to instrument read number in a way
that rules out oxidation as the cause
- ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls
at G reference bases that are correlated to instrument read number in a way
that is consistent with oxidative damage.
- AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
-
- AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of unique bases covered by the intervals of all amplicons in the amplicon set
- ANALYSIS_DIR - Variable in class picard.fastq.BamToBfq
-
- AnnotationException - Exception in picard.annotation
-
Exception thrown when loading gene annotations.
- AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
-
- AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
-
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- areEqual() - Method in class picard.sam.CompareSAMs
-
- areHistogramsEmpty() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
-
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- assertEqualDoubleArrays(double[], double[], double) - Static method in class picard.util.TestNGUtil
-
- assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
- assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
-
- assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Establishes that records returned by this iterator are expected to
be in the specified sort order.
- assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
-
Write into locusFunctions the function of each position from start to start + locusFunctions.length
relative to this transcript.
- ASSUME_SORT_ORDER - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- ASSUME_SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
-
- ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
-
- ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
-
- ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
-
- ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Deprecated.
- ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
-
- ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- AsyncIterator<T> - Class in picard.util
-
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be
efficient.
- AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
-
- AT_DROPOUT - Variable in class picard.analysis.directed.HsMetrics
-
A measure of how undercovered <= 50% GC regions are relative to the mean.
- AT_DROPOUT - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
A measure of how undercovered <= 50% GC regions are relative to the mean.
- AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style AT dropout metric.
- AtomicIterator<T> - Interface in picard.util
-
Describes
- atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
-
- atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
-
- ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
-
- ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
-
- ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
-
- awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Blocks until the work is complete.
- awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
-
- C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
-
- C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
- C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there
were no bias between sites with a C reference base vs.
- C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == C.
- calculateAllGcs(byte[], int, int) - Static method in class picard.analysis.GcBiasUtils
-
- calculateDerivedFields() - Method in class picard.analysis.replicates.IndependentReplicateMetric
-
- calculateDerivedFields() - Method in class picard.analysis.replicates.MergeableMetricBase
-
placeholder method that will calculate the derived fields from the other ones.
- calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
- calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
-
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where
possible and the PERCENT_DUPLICATION.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
Calculate the error rate given the raw counts.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
Calculate the error rate given the raw counts.
- calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) - Static method in class picard.analysis.GcBiasUtils
-
- calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made
If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- CalculateHsMetrics - Class in picard.analysis.directed
-
Deprecated.
- CalculateHsMetrics() - Constructor for class picard.analysis.directed.CalculateHsMetrics
-
Deprecated.
- calculateMatchResults(Fingerprint, Fingerprint, double, double) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed
information about the match (or mismatch) between fingerprints including the LOD score
for whether or not the two are likely from the same sample.
- calculateMatchResults(Fingerprint, Fingerprint) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed
information about the match (or mismatch) between fingerprints including the LOD score
for whether or not the two are likely from the same sample.
- calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made
If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- CalculateReadGroupChecksum - Class in picard.sam
-
- CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
-
- calculateRefWindowsByGc(int, File, int) - Static method in class picard.analysis.GcBiasUtils
-
- calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
-
Calculates a histogram using the estimateRoi method to estimate the effective yield
doing x sequencing for x=1..10.
- calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
-
Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
-
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'call' sample
- CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'call' sample (i.e.
- CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
-
- CallingMetricAccumulator - Class in picard.vcf
-
Collects variants and generates metrics about them.
- CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
-
- CallingMetricAccumulator.Result - Class in picard.vcf
-
- callState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
-
- canMerge(MergeableMetricBase) - Method in class picard.analysis.replicates.MergeableMetricBase
-
checks if this instance can be merged with another
Other must have all the fields that this instance has, and
the fields that are annotated as MergeByAssertEquals must contain the same value
- canSkip() - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
- canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.
- Casava18ReadNameEncoder - Class in picard.fastq
-
A read name encoder conforming to the standard described by Illumina Casava 1.8.
- Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
-
- CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
-
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the
first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read
in a paired run or PAIR when the metrics are aggregated for both first and second reads
in a pair.
- CATEGORY - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
-
One of either WHOLE_GENOME or NON_ZERO_REGIONS
- CHAIN - Variable in class picard.util.LiftOverIntervalList
-
- CHAIN - Variable in class picard.vcf.LiftoverVcf
-
- CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
-
- CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
-
- CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- CHART_OUTPUT - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
-
- CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
-
- CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
-
- CheckFingerprint - Class in picard.fingerprint
-
Attempts to check the sample identity of the sequence data in the provided SAM/BAM file
against a set of known genotypes in the supplied genotype file (in either GELI or VCF format).
- CheckFingerprint() - Constructor for class picard.fingerprint.CheckFingerprint
-
- checkFingerprints(List<File>, List<File>, String, boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Top level method to take a set of one or more SAM files and one or more Genotype files and compare
each read group in each SAM file to each set of fingerprint genotypes.
- CheckIlluminaDirectory - Class in picard.illumina
-
Program to check a lane of an Illumina output directory.
- CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
-
- CheckTerminatorBlock - Class in picard.sam
-
Simple class to check the terminator block of a SAM file.
- CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
-
- CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
-
- ChimeraUtil - Class in picard.analysis
-
- ChimeraUtil() - Constructor for class picard.analysis.ChimeraUtil
-
- CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size
is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
- CHROM - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The chromosome on which the SNP resides.
- CircularByteBuffer - Class in picard.util
-
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic
read/write operations from/to other byte[]s passed as arguments.
- CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
-
Constructs a buffer capable of holding the given number of bytes.
- ClassFinder - Class in picard.cmdline
-
Utility class that can scan for classes in the classpath and find all the ones
annotated with a particular annotation.
- ClassFinder() - Constructor for class picard.cmdline.ClassFinder
-
- ClassFinder(ClassLoader) - Constructor for class picard.cmdline.ClassFinder
-
- ClassFinder(File) - Constructor for class picard.cmdline.ClassFinder
-
- CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN}
(See PFFailSummaryMetric for explanation regarding the possible classification.)
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, int, int) - Static method in class picard.vcf.GenotypeConcordance
-
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int) - Static method in class picard.vcf.GenotypeConcordance
-
Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance
count for the given variant type (SNP or INDEL).
- CleanSam - Class in picard.sam
-
- CleanSam() - Constructor for class picard.sam.CleanSam
-
- CLIP_ADAPTERS - Variable in class picard.fastq.BamToBfq
-
- CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
-
- CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CalculateHsMetrics
-
Deprecated.
- CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectHsMetrics
-
- CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
-
- clipForOverlappingReads(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
-
Checks to see whether the ends of the reads overlap and soft clips reads
them if necessary.
- CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
-
- CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
-
- CLIPPING_MIN_LENGTH - Variable in class picard.sam.SamToFastq
-
- ClippingUtility - Class in picard.util
-
Utilities to clip the adapater sequence from a SAMRecord read
- ClippingUtility() - Constructor for class picard.util.ClippingUtility
-
- ClocsFileFaker - Class in picard.illumina.parser.fakers
-
- ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
-
- ClocsFileReader - Class in picard.illumina.parser.readers
-
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
-
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
-
- close() - Method in interface picard.illumina.IlluminaBasecallsConverter.ConvertedClusterDataWriter
-
- close() - Method in class picard.illumina.parser.IlluminaDataProvider
-
- close() - Method in class picard.illumina.parser.MultiTileFilterParser
-
- close() - Method in class picard.illumina.parser.MultiTileLocsParser
-
- close() - Method in class picard.illumina.parser.PerTileParser
-
- close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
-
- close() - Method in class picard.illumina.parser.readers.BclReader
-
- close() - Method in class picard.illumina.parser.readers.ClocsFileReader
-
- close() - Method in class picard.illumina.parser.readers.LocsFileReader
-
- close() - Method in class picard.illumina.parser.readers.PosFileReader
-
- close() - Method in class picard.sam.AbstractAlignmentMerger
-
- close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- close() - Method in class picard.util.AbstractInputParser
-
Closes this stream and releases any system resources associated with it.
- close() - Method in class picard.util.AsyncIterator
-
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
- close() - Method in class picard.util.BasicInputParser
-
Closes the underlying stream
- close() - Method in class picard.util.CircularByteBuffer
-
Signals that the buffer is closed and no further writes will occur.
- close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- close() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Release all resources associated with the parser.
- close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
-
- close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
-
- close() - Method in class picard.vcf.processor.VariantIteratorProducer
-
- closeWriter() - Method in class picard.sam.FixMateInformation
-
- CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
-
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
- ClusterData - Class in picard.illumina.parser
-
Store the information from Illumina files for a single cluster with one or more reads.
- ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
-
Used for testing, reads is set directly with no copying to the input array
- ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
-
Creates a ClusterData with one read for each type provided
- ClusterDataToSamConverter - Class in picard.illumina
-
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords,
as appropriate, and optionally marking adapter sequence.
- ClusterDataToSamConverter(String, String, ReadStructure, List<IlluminaUtil.IlluminaAdapterPair>) - Constructor for class picard.illumina.ClusterDataToSamConverter
-
Constructor
- code() - Method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
- CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary aligments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
- codingEnd - Variable in class picard.annotation.Gene.Transcript
-
- codingStart - Variable in class picard.annotation.Gene.Transcript
-
- CollectAlignmentSummaryMetrics - Class in picard.analysis
-
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
- CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
-
- CollectBaseDistributionByCycle - Class in picard.analysis
-
- CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
-
- CollectGcBiasMetrics - Class in picard.analysis
-
Tool to collect information about GC bias in the reads in a given BAM file.
- CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
-
- CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
-
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
- CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
-
- CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
-
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
- CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
-
Metrics produced by the GetHiSeqXPFFailMetrics program.
- CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
-
- CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum in picard.illumina.quality
-
- CollectHsMetrics - Class in picard.analysis.directed
-
Collects a set of HS metrics from a sam or bam file.
- CollectHsMetrics() - Constructor for class picard.analysis.directed.CollectHsMetrics
-
- CollectIlluminaBasecallingMetrics - Class in picard.illumina
-
A Command line tool to collect Illumina Basecalling metrics for a sequencing run
Requires a Lane and an input file of Barcodes to expect.
- CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
-
- CollectIlluminaLaneMetrics - Class in picard.illumina
-
- CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
-
- CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
-
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
- CollectIndependentReplicateMetrics - Class in picard.analysis.replicates
-
A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
- CollectIndependentReplicateMetrics() - Constructor for class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- CollectInsertSizeMetrics - Class in picard.analysis
-
Command line program to read non-duplicate insert sizes, create a Histogram
and report distribution statistics.
- CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
-
- CollectJumpingLibraryMetrics - Class in picard.analysis
-
Command-line program to compute metrics about outward-facing pairs, inward-facing
pairs, and chimeras in a jumping library.
- CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
-
- collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
- CollectMultipleMetrics - Class in picard.analysis
-
Class that is designed to instantiate and execute multiple metrics programs that extend
SinglePassSamProgram while making only a single pass through the SAM file and supplying
each program with the records as it goes.
- CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
-
- CollectMultipleMetrics.Program - Enum in picard.analysis
-
- CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
-
- CollectOxoGMetrics - Class in picard.analysis
-
Class for trying to quantify the CpCG->CpCA error rate.
- CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
-
- CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
-
Metrics class for outputs.
- CollectQualityYieldMetrics - Class in picard.analysis
-
Command line program to calibrate quality yield metrics
- CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
-
- CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
-
A set of metrics used to describe the general quality of a BAM file
- CollectRawWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing
experiments, same implementation as CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters
and has much higher coverage cap.
- CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
-
- CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
-
- CollectRnaSeqMetrics - Class in picard.analysis
-
- CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
-
- CollectRrbsMetrics - Class in picard.analysis
-
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well
as CpG sites across all reads in the input BAM/SAM file.
- CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
-
- CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
-
Quantify substitution errors caused by mismatched base pairings during various
stages of sample / library prep.
- CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed
-
Both CollectTargetedPCRMetrics and CalculateHybridSelection metrics share virtually identical program structures except
for the name of their targeting mechanisms (e.g.
- CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
-
- CollectTargetedPcrMetrics - Class in picard.analysis.directed
-
Collect metric information for target pcr metrics runs.
- CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
-
- CollectVariantCallingMetrics - Class in picard.vcf
-
Collects summary and per-sample metrics about variant calls in a VCF file.
- CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
-
- CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
- CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
- CollectWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
- CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
-
- CollectWgsMetrics.WgsMetrics - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetrics.WgsMetricsCollector - Class in picard.analysis
-
- CollectWgsMetricsFromQuerySorted - Class in picard.analysis
-
Deprecated.
- CollectWgsMetricsFromQuerySorted() - Constructor for class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY - Enum in picard.analysis
-
Deprecated.
the various metrics types
- CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics - Class in picard.analysis
-
Deprecated.
Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetricsFromSampledSites - Class in picard.analysis
-
Deprecated.
- CollectWgsMetricsFromSampledSites() - Constructor for class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
- CollectWgsMetricsFromSampledSites.SampledWgsMetrics - Class in picard.analysis
-
Deprecated.
- CollectWgsMetricsWithNonZeroCoverage - Class in picard.analysis
-
- CollectWgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
-
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category - Enum in picard.analysis
-
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector - Class in picard.analysis
-
- COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
-
Implementation note, this is duplicate code stolen from HTSJDK's Default.java
/**
Decides if we want to write colors to the terminal.
- columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
- columnLabelsList() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
- combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
-
- CommandLineDefaults - Class in picard.cmdline
-
Embodies defaults for global values that affect how the Picard Command Line operates.
- CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
-
- CommandLineParseException - Exception in picard.cmdline
-
- CommandLineParseException(String) - Constructor for exception picard.cmdline.CommandLineParseException
-
- CommandLineParseException(String, Throwable) - Constructor for exception picard.cmdline.CommandLineParseException
-
- CommandLineParser - Class in picard.cmdline
-
Annotation-driven utility for parsing command-line arguments, checking for errors, and producing usage message.
- CommandLineParser(Object) - Constructor for class picard.cmdline.CommandLineParser
-
Prepare for parsing command line arguments, by validating annotations.
- CommandLineParser.ClpEnum - Interface in picard.cmdline
-
- CommandLineParser.OptionDefinition - Class in picard.cmdline
-
- CommandLineParser.OptionDefinitionByPrintOrderComparator - Class in picard.cmdline
-
- CommandLineParserDefinitionException - Exception in picard.cmdline
-
- CommandLineParserDefinitionException(String) - Constructor for exception picard.cmdline.CommandLineParserDefinitionException
-
- CommandLineParserDefinitionException(String, Throwable) - Constructor for exception picard.cmdline.CommandLineParserDefinitionException
-
- CommandLineProgram - Class in picard.cmdline
-
Abstract class to facilitate writing command-line programs.
- CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
-
- CommandLineProgramGroup - Interface in picard.cmdline
-
Interface for groups of CommandLinePrograms.
- CommandLineProgramProperties - Annotation Type in picard.cmdline
-
Annotates a command line program with various properties, such as usage (short and long),
as well as to which program group it belongs.
- COMMENT - Variable in class picard.sam.AddCommentsToBam
-
- COMMENT - Variable in class picard.sam.FastqToSam
-
- COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- COMMENT - Variable in class picard.sam.MergeSamFiles
-
- COMMENT - Variable in class picard.util.IntervalListTools
-
- comparator - Static variable in interface picard.cmdline.CommandLineProgramGroup
-
Compares two program groups by name.
- compare(CommandLineParser.OptionDefinition, CommandLineParser.OptionDefinition) - Method in class picard.cmdline.CommandLineParser.OptionDefinitionByPrintOrderComparator
-
- compare(int, int) - Static method in class picard.util.MathUtil
-
- compareDoubleWithAccuracy(double, double, double) - Static method in class picard.util.TestNGUtil
-
Small utility function for determining if two doubles are within a _relative_ accuracy of each other.
- CompareMetrics - Class in picard.analysis
-
Compare two metrics files.
- CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
-
- CompareSAMs - Class in picard.sam
-
Rudimentary SAM comparer.
- CompareSAMs() - Constructor for class picard.sam.CompareSAMs
-
- compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
- compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
- compareTo(Gene) - Method in class picard.annotation.Gene
-
- compareTo(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeBlock
-
- compareTo(MatchResults) - Method in class picard.fingerprint.MatchResults
-
Provides a natural sort so that better matches (by LOD) sort earlier.
- compareTo(Snp) - Method in class picard.fingerprint.Snp
-
- compareTo(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
-
- COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- COMPRESS_OUTPUTS - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
-
- CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- contains(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Returns true if the SNP is contained within the haplotype block, false otherwise.
- contamination - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The sequence context being reported on.
- CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
-
- CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
-
- CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- contig() - Method in class picard.vcf.processor.VcfFileSegment
-
- CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
-
- CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
- convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
-
Creates the SAMRecord for each read in the cluster
- convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.IlluminaBasecallsConverter.ClusterDataConverter
-
Creates the OUTPUT_RECORDs from the cluster
- CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was converted (TG for + strand, CA for - strand)
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
-
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
-
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
-
- ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
-
- ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
-
- convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
-
Converts from Solexa ASCII to Phred binary in place.
- copy(ExtractIlluminaBarcodes.BarcodeMetric) - Static method in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
- CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that map to the correct strand.
- correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
-
- COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
- COUNT_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics
-
- CountingDuplicateFilter - Class in picard.filter
-
Counting filter that discards reads that have been marked as duplicates.
- CountingDuplicateFilter() - Constructor for class picard.filter.CountingDuplicateFilter
-
- CountingFilter - Class in picard.filter
-
A SamRecordFilter that counts the number of bases in the reads which it filters out.
- CountingFilter() - Constructor for class picard.filter.CountingFilter
-
- CountingMapQFilter - Class in picard.filter
-
Counting filter that discards reads below a configurable mapping quality threshold.
- CountingMapQFilter(int) - Constructor for class picard.filter.CountingMapQFilter
-
- CountingPairedFilter - Class in picard.filter
-
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
- CountingPairedFilter() - Constructor for class picard.filter.CountingPairedFilter
-
- Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Constructs a new coverage object for the provided mapping with the desired padding either side.
- COVERAGE_CAP - Variable in class picard.analysis.CollectRawWgsMetrics
-
- COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
-
- COVERAGE_CAP - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- coverageCap - Variable in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
- CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites that were converted (TG for +, CA for -)
- CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites encountered
- CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
-
- CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
-
- CreateHtmlDocForProgram - Class in picard.cmdline
-
Print out the usage for one or more CommandLinePrograms in a form close to what is used in the Sourceforge Picard website.
- CreateHtmlDocForProgram() - Constructor for class picard.cmdline.CreateHtmlDocForProgram
-
- CreateHtmlDocForStandardOptions - Class in picard.cmdline
-
- CreateHtmlDocForStandardOptions() - Constructor for class picard.cmdline.CreateHtmlDocForStandardOptions
-
- createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
-
Soft-clip an alignment that hangs off the end of its reference sequence.
- createSamFileHeader() - Method in class picard.sam.FastqToSam
-
Creates a simple header with the values provided on the command line.
- createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
-
- CreateSequenceDictionary - Class in picard.sam
-
Create a SAM/BAM file from a fasta containing reference sequence.
- CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
-
- createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- CROSSCHECK_LIBRARIES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- CROSSCHECK_SAMPLES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- CrosscheckReadGroupFingerprints - Class in picard.fingerprint
-
Program to check that all read groups within the set of BAM files appear to come from the same
individual.
- CrosscheckReadGroupFingerprints() - Constructor for class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- CsvInputParser - Class in picard.util
-
- CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The name of the amplicon set used in this metrics collection run
- CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
-
- customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
-
- customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
-
- customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
-
- customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
-
- customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.fastq.BamToBfq
-
- customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
-
- customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
-
Validate that POSITION >= 1, and that all BARCODEs are the same length and unique
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
-
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
-
- customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
-
- customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
-
Use reference filename to create URI to go into header if URI was not passed on cmd line.
- customCommandLineValidation() - Method in class picard.sam.FastqToSam
-
- customCommandLineValidation() - Method in class picard.sam.FilterSamReads
-
- customCommandLineValidation() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
-
- customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
-
- customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
-
- customCommandLineValidation() - Method in class picard.sam.RevertSam
-
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
- customCommandLineValidation() - Method in class picard.sam.SamToFastq
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.SetNmAndUqTags
-
- customCommandLineValidation() - Method in class picard.sam.ValidateSamFile
-
- customCommandLineValidation() - Method in class picard.sam.ViewSam
-
- customCommandLineValidation() - Method in class picard.util.BaitDesigner
-
- customCommandLineValidation() - Method in class picard.util.IntervalListTools
-
- customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
-
- CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil
-
- F - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
-
- fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
-
- fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
-
- fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
-
- fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
-
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
-
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
-
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
-
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type create a set of fake files such that the
verification criteria are met.
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
-
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
- Fasta - Class in picard.cmdline.programgroups
-
- Fasta() - Constructor for class picard.cmdline.programgroups.Fasta
-
- FASTQ - Variable in class picard.sam.FastqToSam
-
- FASTQ - Variable in class picard.sam.SamToFastq
-
- FASTQ2 - Variable in class picard.sam.FastqToSam
-
- FastqToSam - Class in picard.sam
-
Converts a fastq file to an unaligned BAM/SAM format.
- FastqToSam() - Constructor for class picard.sam.FastqToSam
-
- FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- FifoBuffer - Class in picard.util
-
A program that is designed to act as a large memory buffer between processes that are
connected with unix pipes where one or more processes either produce or consume their
input or output in bursts.
- FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their
start/end information logged is often undesirable.
- FifoBuffer() - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their
start/end information logged is often undesirable.
- FILE_EXTENSION - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- FILE_EXTENSION - Variable in class picard.analysis.CollectMultipleMetrics
-
- FileChannelJDKBugWorkAround - Class in picard.util
-
Work-around for the following bug
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6503430
Call the method in the main thread before launching threads that do memory-mapping.
- FileChannelJDKBugWorkAround() - Constructor for class picard.util.FileChannelJDKBugWorkAround
-
- FileFaker - Class in picard.illumina.parser.fakers
-
- FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
-
- filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
-
- filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
-
- filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Determine whether or not files are available
- filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
-
- filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Returns only lane and tile information as PerTileFt's do not have End information.
- FILL_POOLS - Variable in class picard.util.BaitDesigner
-
- FILTER - Variable in class picard.sam.FilterSamReads
-
- filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
-
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
-
- filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
-
- filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
-
Test whether or not the genotype should be filtered out.
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
-
- filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
-
- filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
-
Check to see if the VariantContext should have a filter applied to it.
- FILTER_CANNOT_LIFTOVER_INDEL - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target is lifted over, but the reference allele doens't match the new reference.
- FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
-
- FILTER_NO_TARGET - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FilterApplyingVariantIterator - Class in picard.vcf.filter
-
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying
iterator.
- FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
-
Constructs an iterator from an underlying iterator and the provided (possibly empty)
collections of variant and genotype filters.
- FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of indels that are also filtered
- FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of SNPs that are also filtered
- FilterFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
-
- FilterFileReader - Class in picard.illumina.parser.readers
-
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
- FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
-
- filterOut(SAMRecord) - Method in class picard.filter.CountingFilter
-
- filterOut(SAMRecord, SAMRecord) - Method in class picard.filter.CountingFilter
-
- FilterSamReads - Class in picard.sam
-
From a SAM or BAM file, produce a new SAM or BAM by filtering aligned reads or a list of read
names provided in a file (one readname per line)
$Id$
- FilterSamReads() - Constructor for class picard.sam.FilterSamReads
-
- FilterSamReads.Filter - Enum in picard.sam
-
- filterSuspectSites() - Method in class picard.fingerprint.Fingerprint
-
Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach
a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
- FilterVcf - Class in picard.vcf.filter
-
Applies a set of hard filters to Variants and to Genotypes within a VCF.
- FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
-
Constructor to default to having index creation on.
- finalizeAndWriteMetrics(LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
- finalizeMetrics(Map<String, ExtractIlluminaBarcodes.BarcodeMetric>, ExtractIlluminaBarcodes.BarcodeMetric) - Static method in class picard.illumina.ExtractIlluminaBarcodes
-
- find(String, Class<?>) - Method in class picard.cmdline.ClassFinder
-
Scans the classpath for classes within the specified package and sub-packages that
extend the parentType.
- findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
-
Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch
bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
- findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of
one another.
- findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a data type find the most preferred file format even if files are not available
- findTile(int) - Method in class picard.illumina.parser.TileIndex
-
- findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
- Fingerprint - Class in picard.fingerprint
-
Small class to represent a genetic fingerprint as a set of HaplotypeProbabilities
objects that give the relative probabilities of each of the possible haplotypes
at a locus.
- Fingerprint(String, File, String) - Constructor for class picard.fingerprint.Fingerprint
-
- FINGERPRINT_DETAIL_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
-
- FINGERPRINT_SUMMARY_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
-
- FingerprintChecker - Class in picard.fingerprint
-
Major class that coordinates the activities involved in comparing genetic fingerprint
data whether the source is from a genotyping platform or derived from sequence data.
- FingerprintChecker(File) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotypes stored in
the supplied file.
- FingerprintChecker(HaplotypeMap) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotyped provided.
- FingerprintingDetailMetrics - Class in picard.analysis
-
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
- FingerprintingDetailMetrics() - Constructor for class picard.analysis.FingerprintingDetailMetrics
-
- FingerprintingSummaryMetrics - Class in picard.analysis
-
Summary fingerprinting metrics and statistics about the comparison of the sequence data
from a single read group (lane or index within a lane) vs.
- FingerprintingSummaryMetrics() - Constructor for class picard.analysis.FingerprintingSummaryMetrics
-
- FingerprintResults - Class in picard.fingerprint
-
Class that is used to represent the results of comparing a read group within a SAM file
against one or more set of fingerprint genotypes.
- FingerprintResults(File, String) - Constructor for class picard.fingerprint.FingerprintResults
-
- fingerprintSamFile(File, IntervalList) - Method in class picard.fingerprint.FingerprintChecker
-
Generates a Fingerprint per read group in the supplied SAM file using the loci provided in
the interval list.
- fingerprintSamFiles(Collection<File>, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
-
Fingerprints one or more SAM/BAM files at all available loci within the haplotype map, using multiple threads
to speed up the processing.
- finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
-
- finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
-
- finish() - Method in class picard.analysis.CollectGcBiasMetrics
-
- finish() - Method in class picard.analysis.CollectInsertSizeMetrics
-
- finish() - Method in class picard.analysis.CollectQualityYieldMetrics
-
- finish() - Method in class picard.analysis.CollectRnaSeqMetrics
-
- finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
-
- finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
- finish() - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
-
- finish() - Method in class picard.analysis.MeanQualityByCycle
-
- finish() - Method in class picard.analysis.QualityScoreDistribution
-
- finish() - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time finalization work.
- finish() - Method in class picard.metrics.MultiLevelCollector
-
Call finish on all PerUnitMetricCollectors
- finish() - Method in interface picard.metrics.PerUnitMetricCollector
-
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- firstSentence(Doc) - Static method in class picard.util.MetricsDoclet
-
Takes a Doc object and uses the firstSentenceTags() to recreate the first sentence
text.
- FisherStrandFilter - Class in picard.vcf.filter
-
Filters records based on the phred scaled p-value from the Fisher Strand test stored in
the FS attribute.
- FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
-
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
-
- fixGenotypes(GenotypesContext, Map<Allele, Allele>) - Static method in class picard.vcf.LiftoverVcf
-
- FixMateInformation - Class in picard.sam
-
Class to fix mate pair information for all reads in a SAM file.
- FixMateInformation() - Constructor for class picard.sam.FixMateInformation
-
- fixNMandUQ(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Calculates and sets the NM and UQ tags from the record and the reference
- flip() - Method in class picard.fingerprint.Snp
-
Returns a new SNP object with the alleles swapped and MAF corrected.
- FLOWCELL_BARCODE - Variable in class picard.fastq.BamToBfq
-
- FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FN (false negative) count across all variants
- FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.HsMetrics
-
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
the mean coverage level in those targets.
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
the mean coverage level in those targets.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
-
The fold by which the baited region has been amplified above genomic background.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fold by which the amplicon region has been amplified above genomic background.
- foldInto(CollectVariantCallingMetrics.VariantCallingDetailMetrics, Collection<CollectVariantCallingMetrics.VariantCallingDetailMetrics>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
- foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
- FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
-
A Map of file formats to the dataTypes they will provide for this run.
- forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
-
- FourChannelIntensityData - Class in picard.illumina.parser
-
Holds a 4 short values for each cycle of a read.
- FourChannelIntensityData(int) - Constructor for class picard.illumina.parser.FourChannelIntensityData
-
- FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FP (false positive) count across all variants
- FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
-
- FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of fragments in the SAM file
- fromBases(byte[]) - Static method in enum picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromBases(byte, byte) - Static method in enum picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromCode(int) - Static method in enum picard.pedigree.Sex
-
Decodes the Sex from a numeric code.
- fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
-
Attempts to read a pedigree file into memory.
- fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
-
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
- FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
- FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
- FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
- G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
- G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there
were no bias between sites with a C reference base vs.
- G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == G.
- GA4GH_CLIENT_SECRETS - Variable in class picard.cmdline.CommandLineProgram
-
- GA4GHScheme - Class in picard.vcf
-
The scheme is defined in the constructor.
- GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
-
- GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
-
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
- GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
-
- GatherBamFiles - Class in picard.sam
-
Program to perform a rapid "gather" operation on BAM files after a scatter operations where
the same process has been performed on different regions of a BAM file creating many smaller
BAM files that now need to be concatenated back together.
- GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
-
- GatherVcfs - Class in picard.vcf
-
Simple little class that combines multiple VCFs that have exactly the same set of samples
and totally discrete sets of loci.
- GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
-
- GC - Variable in class picard.analysis.GcBiasDetailMetrics
-
The G+C content of the reference sequence represented by this bin.
- GC_DROPOUT - Variable in class picard.analysis.directed.HsMetrics
-
A measure of how undercovered >= 50% GC regions are relative to the mean.
- GC_DROPOUT - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
A measure of how undercovered >= 50% GC regions are relative to the mean.
- GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style GC dropout metric.
- GC_NC_0_19 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content.
- GC_NC_20_39 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
- GC_NC_40_59 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
- GC_NC_60_79 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
- GC_NC_80_100 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
- GcBiasDetailMetrics - Class in picard.analysis
-
Class that holds detailed metrics about reads that fall within windows of a certain
GC bin on the reference genome.
- GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
-
- GcBiasMetrics - Class in picard.metrics
-
- GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
-
- GcBiasMetricsCollector - Class in picard.analysis
-
Calculates GC Bias Metrics on multiple levels
Created by kbergin on 3/23/15.
- GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
-
- GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis
-
- GcBiasSummaryMetrics - Class in picard.analysis
-
High level metrics that capture how biased the coverage in a certain lane is.
- GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
-
- GcBiasUtils - Class in picard.analysis
-
Utilities to calculate GC Bias
Created by kbergin on 9/23/15.
- GcBiasUtils() - Constructor for class picard.analysis.GcBiasUtils
-
- Gene - Class in picard.annotation
-
Holds annotation of a gene for storage in an OverlapDetector.
- Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
-
- Gene.Transcript - Class in picard.annotation
-
A single transcript of a gene.
- Gene.Transcript.Exon - Class in picard.annotation
-
1-based, inclusive representation of an exon.
- GeneAnnotationReader - Class in picard.annotation
-
Load gene annotations into an OverlapDetector of Gene objects.
- GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
-
- generateDataProvider(TestNGUtil.TestNGParameterizable[]) - Static method in class picard.util.TestNGUtil
-
- generateDataProvider(Iterable<? extends TestNGUtil.TestNGParameterizable>) - Static method in class picard.util.TestNGUtil
-
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
-
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
-
- generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
-
Generates a read name string for the provided cluster.
- generateWgsMetrics() - Method in class picard.analysis.CollectRawWgsMetrics
-
- generateWgsMetrics() - Method in class picard.analysis.CollectWgsMetrics
-
- generateWgsMetrics() - Method in class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
- generateWgsMetrics() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
-
- generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
-
- GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
-
- GENOME_SIZE - Variable in class picard.analysis.directed.HsMetrics
-
The number of bases in the reference genome used for alignment.
- GENOME_SIZE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of bases in the reference genome used for alignment.
- GENOME_TERRITORY - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The number of non-N bases in the genome reference over which coverage will be evaluated.
- GENOME_TERRITORY - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The genotype concordance for all possible states.
- GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CheckFingerprint
-
- GenotypeConcordance - Class in picard.vcf
-
Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference)
the other being the call.
- GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
-
- GenotypeConcordanceContingencyMetrics - Class in picard.vcf
-
Class that holds metrics about the Genotype Concordance contingency tables.
- GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
-
- GenotypeConcordanceCounts - Class in picard.vcf
-
A class to store the counts for various truth and call state classifications relative to a reference.
- GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
-
- GenotypeConcordanceDetailMetrics - Class in picard.vcf
-
Class that holds detail metrics about Genotype Concordance
- GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
-
- GenotypeConcordanceScheme - Class in picard.vcf
-
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
- GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
-
- GenotypeConcordanceSchemeFactory - Class in picard.vcf
-
Created by kbergin on 6/19/15.
- GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
-
- GenotypeConcordanceStateCodes - Enum in picard.vcf
-
Created by kbergin on 7/30/15.
- GenotypeConcordanceStates - Class in picard.vcf
-
A class to store the various classifications for:
1.
- GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
-
- GenotypeConcordanceStates.CallState - Enum in picard.vcf
-
These states represent the relationship between the call genotype and the truth genotype relative to
a reference sequence.
- GenotypeConcordanceStates.ContingencyState - Enum in picard.vcf
-
A specific state for a 2x2 contingency table.
- GenotypeConcordanceStates.TruthAndCallStates - Class in picard.vcf
-
A minute class to store the truth and call state respectively.
- GenotypeConcordanceStates.TruthState - Enum in picard.vcf
-
These states represent the relationship between a truth genotype and the reference sequence.
- GenotypeConcordanceSummaryMetrics - Class in picard.vcf
-
Class that holds summary metrics about Genotype Concordance
- GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
-
- GenotypeFilter - Interface in picard.vcf.filter
-
An interface for classes that perform Genotype filtration.
- GenotypeQualityFilter - Class in picard.vcf.filter
-
Genotype filter that filters out genotypes below a given quality threshold.
- GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
-
- GenotypeReader - Class in picard.fingerprint
-
- GenotypeReader() - Constructor for class picard.fingerprint.GenotypeReader
-
Deprecated.
- GenotypeReader.VariantIterator - Class in picard.fingerprint
-
Deprecated.
Small class to encapsulate an iterator over variants, optionally with a sequence dictionary.
- GENOTYPES - Variable in class picard.fingerprint.CheckFingerprint
-
- GENOTYPING_ERROR_RATE - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
-
- get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- get3PrimeAdapter() - Method in interface picard.util.AdapterPair
-
- get3PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
-
- get3PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
-
- get3PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
-
- get3PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get5PrimeAdapter() - Method in interface picard.util.AdapterPair
-
- get5PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
-
- get5PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
-
- get5PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
-
- get5PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- getA() - Method in class picard.illumina.parser.FourChannelIntensityData
-
- getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Get the available tiles for the given formats, if the formats have tile lists that differ then
throw an exception, if any of the format
- getAllele1() - Method in enum picard.fingerprint.DiploidGenotype
-
- getAllele1() - Method in class picard.fingerprint.Snp
-
- getAllele2() - Method in enum picard.fingerprint.DiploidGenotype
-
- getAllele2() - Method in class picard.fingerprint.Snp
-
- getAlleleString() - Method in class picard.fingerprint.Snp
-
- getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
-
Get the PerUnitMetricCollector that collects reads for all levels
- getAllSnps() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
- getArgv() - Method in class picard.cmdline.CommandLineParser
-
- getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Return the list of tiles available for this flowcell and lane.
- getBarcodeValue(SAMRecord) - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- getBases() - Method in class picard.illumina.parser.BclData
-
- getBases() - Method in class picard.illumina.parser.ReadData
-
- getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetrics
-
If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the
edge.
- getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
By design we want to count just those bases at the positions we care about, not across the entire read.
- getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
-
- getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
-
Returns the number of bytes that are in the buffer at the time of the method invocation.
- getC() - Method in class picard.illumina.parser.FourChannelIntensityData
-
- getCallerOptions() - Method in class picard.cmdline.CommandLineParser
-
- getCapacity() - Method in class picard.util.CircularByteBuffer
-
Returns the total capacity of the buffer (empty+filled).
- getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
We have to re-chain the program groups based on this algorithm.
- getChannel(IntensityChannel) - Method in class picard.illumina.parser.FourChannelIntensityData
-
- getChrom() - Method in class picard.fingerprint.Snp
-
- getClasses() - Method in class picard.cmdline.ClassFinder
-
Fetches the set of classes discovered so far.
- getClusterCount() - Method in class picard.illumina.parser.Tile
-
Returns the number of on this tile.
- getClusterDensity() - Method in class picard.illumina.parser.Tile
-
Returns the cluster density of this tile, in units of [cluster/mm^2].
- getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.CallState
-
- getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.TruthState
-
- getCollector(int) - Method in class picard.analysis.CollectWgsMetrics
-
- getCollector(int) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
-
- getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
- getCommandLine() - Method in class picard.cmdline.CommandLineParser
-
The commandline used to run this program, including any default args that
weren't necessarily specified.
- getCommandLine() - Method in class picard.cmdline.CommandLineProgram
-
- getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
-
- getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
- getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a set
- getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a parse-able string
- getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
-
- getCurrentLine() - Method in class picard.util.BasicInputParser
-
Provides access to the current (just parsed) line in pre-parsed format.
- getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
-
- getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
-
- getCurrentLineNumber() - Method in class picard.util.BasicInputParser
-
NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the
next line, not the most recent line returned by next().
- getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
- getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
-
- getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
-
- getDepthHistogram() - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Gets the coverage depths as an array of ints.
- getDescription() - Method in interface picard.cmdline.CommandLineProgramGroup
-
Gets the description of this program.
- getDescription() - Method in class picard.cmdline.programgroups.Alpha
-
- getDescription() - Method in class picard.cmdline.programgroups.Fasta
-
- getDescription() - Method in class picard.cmdline.programgroups.Illumina
-
- getDescription() - Method in class picard.cmdline.programgroups.Intervals
-
- getDescription() - Method in class picard.cmdline.programgroups.Metrics
-
- getDescription() - Method in class picard.cmdline.programgroups.None
-
- getDescription() - Method in class picard.cmdline.programgroups.SamOrBam
-
- getDescription() - Method in class picard.cmdline.programgroups.Testing
-
- getDescription() - Method in class picard.cmdline.programgroups.VcfOrBcf
-
- getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- getDiploidHaplotype(Snp, DiploidGenotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the diploid haplotype for this haplotype block given the provided SNP and SNP
genotype.
- getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
- getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getFactory() - Method in class picard.illumina.IlluminaBasecallsConverter
-
In case caller needs to get some info from factory.
- getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
-
- getFaqLink() - Static method in class picard.cmdline.CommandLineParser
-
- getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
-
- getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
-
- getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
-
- getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
-
- getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- getFile() - Method in class picard.illumina.parser.TileIndex
-
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
- getFileName() - Method in class picard.util.AbstractInputParser
-
- getFileName() - Method in class picard.util.BasicInputParser
-
Gets the name of the file being parsed
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
-
- getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
-
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
-
- getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created
on util instantiation, doesn't contain any of these tiles/cycles).
- getFilteredBases() - Method in class picard.filter.CountingFilter
-
Gets the number of bases that have been filtered out thus far.
- getFilteredRecords() - Method in class picard.filter.CountingFilter
-
Gets the number of records that have been filtered out thus far.
- getFingerprintFile() - Method in class picard.fingerprint.MatchResults
-
- getFingerprintPanels() - Method in class picard.fingerprint.Snp
-
- getFirstSnp() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the arbitrarily first SNP in the haplotype.
- getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- getForceSort() - Method in class picard.sam.SamAlignmentMerger
-
- getFractionUnexpectedAlleleObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
- getG() - Method in class picard.illumina.parser.FourChannelIntensityData
-
- getGene() - Method in class picard.annotation.Gene.Transcript
-
- getHaplotype(Snp) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp object.
- getHaplotype(String) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp name.
- getHaplotype(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp chromosome and position.
- getHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the haplotype for which the probabilities apply.
- getHaplotypeFrequencies() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the set of haplotype frequencies.
- getHaplotypeFrequency(int) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding
to DiploidHaplotype.
- getHaplotypes() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all the haplotype blocks in the map.
- getHeader() - Method in class picard.fingerprint.FingerprintChecker
-
- getHeader() - Method in class picard.fingerprint.GenotypeReader.VariantIterator
-
Deprecated.
- getHeader() - Method in class picard.fingerprint.HaplotypeMap
-
- getHeader() - Method in class picard.sam.AbstractAlignmentMerger
-
- getHelpDoc() - Method in interface picard.cmdline.CommandLineParser.ClpEnum
-
- getHelpDoc() - Method in enum picard.util.IntervalListTools.Action
-
- getHet(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
-
- getHeterogyzousGenotype() - Method in class picard.fingerprint.Snp
-
- getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
-
- getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
-
- getHomozygousAllele1Genotype() - Method in class picard.fingerprint.Snp
-
- getHomozygousAllele2Genotype() - Method in class picard.fingerprint.Snp
-
- getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
-
- getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
-
- getInfo() - Method in class picard.fingerprint.Fingerprint
-
- getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
-
- getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
-
- getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- getIntervalList() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
- getLane() - Method in class picard.illumina.parser.ClusterData
-
- getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the lane we're inspecting
- getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
-
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- getLaneNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number of this tile's parent lane.
- getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- getLastThreeFields(String, char, int[]) - Static method in class picard.sam.util.ReadNameParser
-
Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
- getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Get the library ID for the given SAM record.
- getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
-
- getLibraryId() - Method in interface picard.sam.util.PhysicalLocation
-
- getLibraryId() - Method in class picard.sam.util.PhysicalLocationInt
-
- getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Gets the library name from the header for the record.
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
Mathematically this is P(evidence | haplotype) where haplotype={AA,Aa,aa}.
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
- getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- getLociToGenotype(Collection<Fingerprint>) - Method in class picard.fingerprint.FingerprintChecker
-
Takes a set of fingerprints and returns an IntervalList containing all the loci that
can be productively examined in sequencing data to compare to one or more of the
fingerprints.
- getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetrics
-
- getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
- getLocusResults() - Method in class picard.fingerprint.MatchResults
-
- getLOD() - Method in class picard.fingerprint.MatchResults
-
- getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the LOD score between the most probable haplotype and the second most probable.
- getLodNT() - Method in class picard.fingerprint.MatchResults
-
- getLodTN() - Method in class picard.fingerprint.MatchResults
-
- getLog_of_base() - Method in class picard.util.MathUtil.LogMath
-
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
- getLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal value.
- getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal array.
- getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- getMaf() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the minor allele frequency of this haplotype.
- getMaf() - Method in class picard.fingerprint.Snp
-
- getMappingsDiffer() - Method in class picard.sam.CompareSAMs
-
- getMappingsMatch() - Method in class picard.sam.CompareSAMs
-
- getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
-
Returns the total of soft or hard masked bases in the interval of bases.
- getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
-
- getMatchResults() - Method in class picard.fingerprint.FingerprintResults
-
- getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
-
- getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
-
- getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
-
- getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
-
- getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
-
- getMessage(int) - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
-
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- getMetrics(Histogram<Integer>, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getMetricsCode() - Method in enum picard.illumina.parser.IlluminaMetricsCode
-
- getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
-
Gets a MetricsFile with default headers already written into it.
- getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- getMinPairMatchBases() - Method in class picard.util.AdapterMarker
-
- getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
-
- getMissingLeft() - Method in class picard.sam.CompareSAMs
-
- getMissingRight() - Method in class picard.sam.CompareSAMs
-
- getMostLikelyGenotype(Snp) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the genotype for this Snp given the most likely haplotype.
- getMostLikelyHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the most likely haplotype given the probabilities.
- getName() - Method in interface picard.cmdline.CommandLineProgramGroup
-
Gets the name of this program.
- getName() - Method in class picard.cmdline.programgroups.Alpha
-
- getName() - Method in class picard.cmdline.programgroups.Fasta
-
- getName() - Method in class picard.cmdline.programgroups.Illumina
-
- getName() - Method in class picard.cmdline.programgroups.Intervals
-
- getName() - Method in class picard.cmdline.programgroups.Metrics
-
- getName() - Method in class picard.cmdline.programgroups.None
-
- getName() - Method in class picard.cmdline.programgroups.SamOrBam
-
- getName() - Method in class picard.cmdline.programgroups.Testing
-
- getName() - Method in class picard.cmdline.programgroups.VcfOrBcf
-
- getName() - Method in class picard.fingerprint.Snp
-
- getName() - Method in interface picard.util.AdapterPair
-
- getName() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
- getNearProbeDistance() - Method in class picard.analysis.directed.TargetMetricsCollector
-
Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- getNestedOptions() - Method in class picard.cmdline.CommandLineProgram
-
- getNestedOptionsForHelp() - Method in class picard.cmdline.CommandLineProgram
-
- getNextReadPair(PeekableIterator<SAMRecord>) - Static method in class picard.util.QuerySortedReadPairIteratorUtil
-
Get the next read pair (where both have the same read name).
- getNoise() - Method in class picard.illumina.parser.ReadData
-
- getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the decimal representation of the provided log values.
- getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
-
- getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
- getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
-
- getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
-
- getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
-
- getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the number of duplicates detected
- getNumReads() - Method in class picard.illumina.parser.ClusterData
-
- getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Useful for statistics after the iterator has been exhausted and closed.
- getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
-
- getNumTiles() - Method in class picard.illumina.parser.TileIndex
-
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the first/major haplotype allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the first allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the second/minor haplotype allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the second allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
-
Returns a single byte that encodes the orientation of the two reads in a pair.
- getOutput(RootDoc) - Static method in class picard.util.MetricsDoclet
-
Gets the file output parameter from the RootDoc and then opens an
PrintStream to write to the file.
- getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
-
- getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
-
- getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
-
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
- getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
-
Return an index that where:
index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases)
an array index into a two dimensional array of byte[][] where the top level array corresponds to read number
index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element
in an array as described above
- getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
-
- getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input
readStructure
- getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
-
- getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- getPackageList() - Static method in class picard.cmdline.PicardCommandLine
-
The packages we wish to include in our command line
- getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
-
- getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through
all the files for these tiles in expectedBase
Side Effect: Assigns numCycles
- getPhasingCode(int, IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
-
Phasing codes are between 200 and 299 (inclusive).
- getPhasingMap() - Method in class picard.illumina.parser.Tile
-
- getPhasingMetricsForTiles(long, Collection<Tile>) - Static method in class picard.illumina.IlluminaPhasingMetrics
-
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
- getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
-
- getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
-
- getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
- getPopulationLikelihood() - Method in class picard.fingerprint.MatchResults
-
- getPos() - Method in class picard.fingerprint.Snp
-
- getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the posterior probabilities using the population frequency as a prior.
- getPrePhasingMap() - Method in class picard.illumina.parser.Tile
-
- getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
-
- getPrintableId() - Method in class picard.fingerprint.Fingerprint
-
- getPriorProbablities() - Method in class picard.fingerprint.HaplotypeProbabilities
-
- getProbeIntervals() - Method in class picard.analysis.directed.CollectHsMetrics
-
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
-
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
-
- getProbeSetName() - Method in class picard.analysis.directed.CollectHsMetrics
-
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
-
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
-
- getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
-
- getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
-
- getQualities() - Method in class picard.illumina.parser.BclData
-
- getQualities() - Method in class picard.illumina.parser.ReadData
-
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
-
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
-
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
- getRawIntensities() - Method in class picard.illumina.parser.ReadData
-
- getRead(int) - Method in class picard.illumina.parser.ClusterData
-
- getReadBarcodeValue(SAMRecord, String) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Gets the set of read ends
- getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Gets the read ends for optical duplicate tracking
- getReadGroup() - Method in class picard.fingerprint.FingerprintResults
-
- getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
-
- getReadGroup() - Method in interface picard.sam.util.PhysicalLocation
-
- getReadGroup() - Method in class picard.sam.util.PhysicalLocationInt
-
- getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
- getReadType() - Method in class picard.illumina.parser.ReadData
-
- getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
-
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns a representative SNP for this haplotype.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
Returns the SNP who's genotype was used to construct the likelihoods.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- getSamFile() - Method in class picard.fingerprint.FingerprintResults
-
- getSamFileHeader() - Method in class picard.analysis.CollectWgsMetrics
-
- getSample() - Method in class picard.fingerprint.Fingerprint
-
- getSample() - Method in class picard.fingerprint.MatchResults
-
- getSampleLikelihood() - Method in class picard.fingerprint.MatchResults
-
- getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
-
- getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
A number of convenience functions
- getScatteredFileName(File, long, String) - Static method in class picard.util.IntervalListTools
-
- getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
-
- getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sensitivity defined by the scheme across the subset of truth states.
- getSequenceDictionary() - Method in class picard.fingerprint.GenotypeReader.VariantIterator
-
Deprecated.
- getSequenceDictionary() - Method in class picard.sam.AbstractAlignmentMerger
-
- getSequentialFileList(File) - Static method in class picard.sam.FastqToSam
-
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
- getSex() - Method in class picard.pedigree.PedFile.PedTrio
-
- getSingletonSample(VariantContext) - Static method in class picard.vcf.CallingMetricAccumulator
-
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- getSnp(String) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets a SNP by name if it belongs to this haplotype.
- getSnp(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a Snp by chromosome and position.
- getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
-
- getSnpGenotype(Snp, DiploidHaplotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the expected genotype of the provided SNP given the provided haplotype of this
haplotype block.
- getSnps() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
- getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
-
Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order:
[cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
- getSource() - Method in class picard.fingerprint.Fingerprint
-
- getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the specificity defined by the scheme across the subset of truth states.
- getStandardUsagePreamble(Class) - Static method in class picard.cmdline.CommandLineParser
-
A typical command line program will call this to get the beginning of the usage message,
and then append a description of the program, like this:
\@Usage
public String USAGE = CommandLineParser.getStandardUsagePreamble(getClass()) + "Frobnicates the freebozzle."
- getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
-
- getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getT() - Method in class picard.illumina.parser.FourChannelIntensityData
-
- getTestcases() - Method in class picard.util.TestNGUtil.SingleTestUnitTest
-
- getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
-
- getTile() - Method in class picard.illumina.parser.ClusterData
-
- getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- getTile() - Method in interface picard.sam.util.PhysicalLocation
-
- getTile() - Method in class picard.sam.util.PhysicalLocationInt
-
- getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return all files that match pattern of the given file type in the given base directory
- getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
-
Parse the tile # from the read name.
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
-
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- getTileNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number/name of this tile.
- getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
-
- getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
-
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
- getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
-
- getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
-
- getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a list of all tiles available for this file format and run
- getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Discover all files of this type in expectedBase that match pattern and construct a list of tiles
available based on these files.
- getTiles() - Method in class picard.illumina.parser.TileIndex
-
- getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
-
- getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
- getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
- getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
-
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the total number of observations of any allele.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Gets the total number of observations presented at this locus.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
-
- getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
-
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
- getUnmappedBoth() - Method in class picard.sam.CompareSAMs
-
- getUnmappedLeft() - Method in class picard.sam.CompareSAMs
-
- getUnmappedRight() - Method in class picard.sam.CompareSAMs
-
- getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Given a file type, get the Parameterized File Util object associated with it
- getVar(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
-
- getVariantTypeFromOrdinal(int) - Static method in enum picard.util.VariantType
-
Gets the enum for a given ordinal
- getVersion() - Method in class picard.cmdline.CommandLineParser
-
- getVersion() - Method in class picard.cmdline.CommandLineProgram
-
- getWordCount() - Method in class picard.util.AbstractInputParser
-
- getX() - Method in class picard.illumina.parser.ClusterData
-
- getX() - Method in interface picard.sam.util.PhysicalLocation
-
- getX() - Method in class picard.sam.util.PhysicalLocationInt
-
- getY() - Method in class picard.illumina.parser.ClusterData
-
- getY() - Method in interface picard.sam.util.PhysicalLocation
-
- getY() - Method in class picard.sam.util.PhysicalLocationInt
-
- getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
-
- GVCF_INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
-
- GvcfMetricAccumulator - Class in picard.vcf
-
An accumulator for collecting metrics about a single-sample GVCF.
- GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.GvcfMetricAccumulator
-
- handleItem(String) - Method in class picard.cmdline.ClassFinder
-
Checks an item to see if it is a class and is annotated with the specified
annotation.
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CheckFingerprint
-
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- HaplotypeBlock - Class in picard.fingerprint
-
Represents information about a group of SNPs that form a haplotype in perfect LD
with one another.
- HaplotypeBlock(double) - Constructor for class picard.fingerprint.HaplotypeBlock
-
Constructs a haplotype block with the provided minor allele frequency.
- HaplotypeMap - Class in picard.fingerprint
-
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data
to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
- HaplotypeMap(File) - Constructor for class picard.fingerprint.HaplotypeMap
-
Constructs a HaplotypeMap from the provided file.
- HaplotypeMap(SAMFileHeader) - Constructor for class picard.fingerprint.HaplotypeMap
-
Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
- HaplotypeProbabilities - Class in picard.fingerprint
-
Abstract class for storing and calculating various likelihoods and probabilities
for haplotype alleles given evidence.
- HaplotypeProbabilities(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilities
-
- HaplotypeProbabilities.Genotype - Enum in picard.fingerprint
-
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes
{aa, ab, bb}
- HaplotypeProbabilitiesFromContaminatorSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype of the contaminating sample given the data.
- HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
- HaplotypeProbabilitiesFromGenotype - Class in picard.fingerprint
-
Represents a set of HaplotypeProbabilities that were derived from a single SNP
genotype at a point in time.
- HaplotypeProbabilitiesFromGenotype(Snp, HaplotypeBlock, double, double, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
- HaplotypeProbabilitiesFromGenotypeLikelihoods - Class in picard.fingerprint
-
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood)
for each of the SNPs in that block.
- HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
- HaplotypeProbabilitiesFromSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype given the data.
- HaplotypeProbabilitiesFromSequence(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
- HaplotypeProbabilityOfNormalGivenTumor - Class in picard.fingerprint
-
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and
provide an hp for the normal sample that tumor came from.
- HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- HAPLOTYPES_CONFIDENTLY_CHECKED - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of genotyped haplotypes for which there was sufficient sequence data to
confidently genotype the haplotype.
- HAPLOTYPES_CONFIDENTLY_MATCHING - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of confidently checked haplotypes that match the expected genotypes.
- HAPLOTYPES_WITH_GENOTYPES - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The number of haplotypes that had expected genotypes to compare to.
- hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
-
True if this record has paternal and maternal ids, otherwise false.
- hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
-
- hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Returns true if any base in the range has coverage of > 0
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns true if evidence has been added, false if the probabilities are just the priors.
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- hashCode() - Method in class picard.annotation.Gene.Transcript
-
- hashCode() - Method in class picard.fingerprint.HaplotypeBlock
-
- hashCode() - Method in class picard.fingerprint.Snp
-
- hashCode() - Method in class picard.illumina.parser.FourChannelIntensityData
-
- hashCode() - Method in class picard.illumina.parser.Range
-
- hashCode() - Method in class picard.illumina.parser.ReadDescriptor
-
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
-
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- hashCode() - Method in class picard.illumina.parser.ReadStructure
-
- hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- hashCode() - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
-
- hasLocation() - Method in interface picard.sam.util.PhysicalLocation
-
Default implementation of a method to check whether real location data has been set.
- hasNext() - Method in class picard.illumina.parser.IlluminaDataProvider
-
- hasNext() - Method in class picard.illumina.parser.MultiTileParser
-
- hasNext() - Method in class picard.illumina.parser.PerTileParser
-
- hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Return true if the file has more elements to return, false otherwise
- hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
-
- hasNext() - Method in class picard.illumina.parser.readers.BclReader
-
- hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
-
- hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
-
- hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
-
- hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
-
- hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
-
- hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- hasNext() - Method in class picard.util.AsyncIterator
-
- hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
-
- hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
-
- hasNext() - Method in class picard.vcf.PairedVariantSubContextIterator
-
- hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
-
- hasWebDocumentation(Class) - Static method in class picard.cmdline.CommandLineParser
-
Determines if a class has web documentation based on its package name
- header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
-
- HEADER - Variable in class picard.sam.ReplaceSamHeader
-
- HEADER_ONLY - Variable in class picard.sam.ViewSam
-
- headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
-
- headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
-
- headerLines() - Method in class picard.vcf.filter.QdFilter
-
- headerLines() - Method in interface picard.vcf.filter.VariantFilter
-
Return VCF header lines that define filters that may be applied by the VariantFilter.
- HET_AS_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of hets, observed as homs with LOD > threshold
- HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
(count of hets)/(count of homozygous non-ref) for this sample
- HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
- HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
- HET_SNP_Q - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_Q - Variable in class picard.analysis.directed.HsMetrics
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_Q - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.HsMetrics
-
The theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The theoretical HET SNP sensitivity.
- HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all heterozygous variants cannot be calculated
- hetAltDepthDistribution(int) - Static method in class picard.analysis.TheoreticalSensitivity
-
- hetSNPSensitivity(double[], double[], int, double) - Static method in class picard.analysis.TheoreticalSensitivity
-
- hetSNPSensitivity(double[], double[], int, double, boolean) - Static method in class picard.analysis.TheoreticalSensitivity
-
- Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
-
- Histogram_R_SCRIPT - Static variable in class picard.analysis.CollectInsertSizeMetrics
-
- HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
-
- histogramArray - Variable in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
-
- HOM_AS_HET - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as hets with LOD > threshold
- HOM_AS_OTHER_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as other homs with LOD > threshold
- HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
- HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
- HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all homozygous variants cannot be calculated.
- HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
-
The estimated number of unique molecules in the selected part of the library.
- HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
- HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
- HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
- HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
- HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
- HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
- HsMetricCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
-
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
-
- HsMetrics - Class in picard.analysis.directed
-
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
- HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics
-
- htmlPrintOptions(PrintStream, boolean) - Method in class picard.cmdline.CommandLineParser
-
- htmlUsage(PrintStream, String, boolean) - Method in class picard.cmdline.CommandLineParser
-
- identifyContaminant(File, double, int) - Method in class picard.fingerprint.FingerprintChecker
-
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
- IGNORE - Variable in class picard.sam.ValidateSamFile
-
- IGNORE_MISSING_MATES - Variable in class picard.sam.FixMateInformation
-
- IGNORE_READ_GROUPS - Variable in class picard.fingerprint.CheckFingerprint
-
- IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- IGNORE_THIS_PROPERTY - Variable in class picard.cmdline.CommandLineParser
-
This attribute is here just to facilitate printing usage for OPTIONS_FILE
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
-
- ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
-
- ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
-
For now, we only ignore those alignments that have more than maxGaps insertions
or deletions.
- IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of primary alignments that map to a sequence specified on command-line as IGNORED_SEQUENCE.
- Illumina - Class in picard.cmdline.programgroups
-
- Illumina() - Constructor for class picard.cmdline.programgroups.Illumina
-
- ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
- IlluminaBasecallingMetrics - Class in picard.illumina
-
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
- IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
-
- IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
Manages the conversion of Illumina basecalls into some output format.
- IlluminaBasecallsConverter(File, int, ReadStructure, Map<String, ? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean) - Constructor for class picard.illumina.IlluminaBasecallsConverter
-
- IlluminaBasecallsConverter(File, File, int, ReadStructure, Map<String, ? extends IlluminaBasecallsConverter.ConvertedClusterDataWriter<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, boolean, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean) - Constructor for class picard.illumina.IlluminaBasecallsConverter
-
- IlluminaBasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
-
- IlluminaBasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
-
- IlluminaBasecallsToFastq - Class in picard.illumina
-
- IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
-
- IlluminaBasecallsToFastq.ReadNameFormat - Enum in picard.illumina
-
Simple switch to control the read name format to emit.
- IlluminaBasecallsToSam - Class in picard.illumina
-
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into
SAM or BAM file format.
- IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
-
- IlluminaDataProvider - Class in picard.illumina.parser
-
Parse various formats and versions of Illumina Basecall files, and use them the to populate
ClusterData objects.
- IlluminaDataProviderFactory - Class in picard.illumina.parser
-
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an
IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
- IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, IlluminaDataType...) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, IlluminaDataType...) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataType - Enum in picard.illumina.parser
-
List of data types of interest when parsing Illumina data.
- IlluminaFileUtil - Class in picard.illumina.parser
-
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
- IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
-
- IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
-
- IlluminaFileUtil.SupportedIlluminaFormat - Enum in picard.illumina.parser
-
- IlluminaLaneMetrics - Class in picard.illumina
-
Embodies characteristics that describe a lane.
- IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
-
- IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
- IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
-
- IlluminaMetricsCode - Enum in picard.illumina.parser
-
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code
(e.g.
- IlluminaPhasingMetrics - Class in picard.illumina
-
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
- IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
-
- IlluminaReadNameEncoder - Class in picard.fastq
-
A read name encoder following the encoding initially produced by picard fastq writers.
- IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
-
- IlluminaTileMetrics(ByteBuffer) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
-
- IlluminaUtil - Class in picard.util
-
Misc utilities for working with Illumina specific files and data
- IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
-
- IlluminaUtil.IlluminaAdapterPair - Enum in picard.util
-
Describes adapters used on each pair of strands
- in - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
-
- INCLUDE_DUPLICATES - Variable in class picard.analysis.CollectInsertSizeMetrics
-
- INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
-
- INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
-
- INCLUDE_NON_PF_READS - Variable in class picard.fastq.BamToBfq
-
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
-
- INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
-
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
-
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
-
- INCLUDE_SUPPLEMENTAL_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
-
- INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that map to the incorrect strand.
- increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Increments a count for the truth/call state tuple.
- increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
-
- incrementReadCount() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Increments the # of reads mapping to this target.
- INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
-
- indelCounter - Variable in class picard.vcf.GenotypeConcordance
-
- indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
-
- IndependentReplicateMetric - Class in picard.analysis.replicates
-
A class to store information relevant for biological rate estimation
- IndependentReplicateMetric() - Constructor for class picard.analysis.replicates.IndependentReplicateMetric
-
- independentReplicationRateFromBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- independentReplicationRateFromTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- independentReplicationRateFromUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- INDEX_VALIDATION_STRINGENCY - Variable in class picard.sam.ValidateSamFile
-
- indexOfMax(double[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- indexOfMax(long[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- initialize() - Method in class picard.illumina.parser.MultiTileBclParser
-
- initiateScheme() - Method in class picard.vcf.GA4GHScheme
-
- initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
-
- initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
-
- INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
-
- INPUT - Variable in class picard.analysis.CollectMultipleMetrics
-
- INPUT - Variable in class picard.analysis.CollectOxoGMetrics
-
- INPUT - Variable in class picard.analysis.CollectRrbsMetrics
-
- INPUT - Variable in class picard.analysis.CollectWgsMetrics
-
- INPUT - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- INPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- INPUT - Variable in class picard.analysis.SinglePassSamProgram
-
- INPUT - Variable in class picard.fastq.BamToBfq
-
- INPUT - Variable in class picard.fingerprint.CheckFingerprint
-
- INPUT - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
- INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
-
- INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
-
- INPUT - Variable in class picard.reference.NonNFastaSize
-
- INPUT - Variable in class picard.reference.NormalizeFasta
-
- INPUT - Variable in class picard.sam.AddCommentsToBam
-
- INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
-
- INPUT - Variable in class picard.sam.BamIndexStats
-
- INPUT - Variable in class picard.sam.BuildBamIndex
-
- INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
-
- INPUT - Variable in class picard.sam.CheckTerminatorBlock
-
- INPUT - Variable in class picard.sam.CleanSam
-
- INPUT - Variable in class picard.sam.DownsampleSam
-
- INPUT - Variable in class picard.sam.FilterSamReads
-
- INPUT - Variable in class picard.sam.FixMateInformation
-
- INPUT - Variable in class picard.sam.GatherBamFiles
-
- INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- INPUT - Variable in class picard.sam.MergeSamFiles
-
- INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
-
- INPUT - Variable in class picard.sam.ReorderSam
-
- INPUT - Variable in class picard.sam.ReplaceSamHeader
-
- INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
- INPUT - Variable in class picard.sam.RevertSam
-
- INPUT - Variable in class picard.sam.SamFormatConverter
-
- INPUT - Variable in class picard.sam.SamToFastq
-
- INPUT - Variable in class picard.sam.SetNmAndUqTags
-
- INPUT - Variable in class picard.sam.SortSam
-
- INPUT - Variable in class picard.sam.SplitSamByLibrary
-
- INPUT - Variable in class picard.sam.ValidateSamFile
-
- INPUT - Variable in class picard.sam.ViewSam
-
- INPUT - Variable in class picard.util.BedToIntervalList
-
- INPUT - Variable in class picard.util.IntervalListToBed
-
- INPUT - Variable in class picard.util.IntervalListTools
-
- INPUT - Variable in class picard.util.LiftOverIntervalList
-
- INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
-
- INPUT - Variable in class picard.vcf.filter.FilterVcf
-
- INPUT - Variable in class picard.vcf.GatherVcfs
-
- INPUT - Variable in class picard.vcf.LiftoverVcf
-
- INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
-
- INPUT - Variable in class picard.vcf.MergeVcfs
-
- INPUT - Variable in class picard.vcf.RenameSampleInVcf
-
- INPUT - Variable in class picard.vcf.SortVcf
-
- INPUT - Variable in class picard.vcf.SplitVcfs
-
- INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
-
- INPUT - Variable in class picard.vcf.VcfFormatConverter
-
- INPUT - Variable in class picard.vcf.VcfToIntervalList
-
- INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
-
- INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- InsertSizeMetrics - Class in picard.analysis
-
Metrics about the insert size distribution of a paired-end library, created by the
CollectInsertSizeMetrics program and usually written to a file with the extension
".insert_size_metrics".
- InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
-
- InsertSizeMetricsCollector - Class in picard.analysis.directed
-
Collects InserSizeMetrics on the specified accumulationLevels using
- InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, double, boolean) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
-
- InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
-
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
- instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
-
- instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
-
The main method.
- instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
-
For testing
- instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
-
- IntensityChannel - Enum in picard.illumina.parser
-
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader,
for cases in which it is desirable to handle these abstractly rather than having the specific names
in the source code.
- INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary aligments that do not align to any gene.
- INTERLEAVE - Variable in class picard.sam.SamToFastq
-
- INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The path to the directory containing the tile metrics file relative to the basecalling directory.
- INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
-
- INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
-
- INTERVAL_LIST - Variable in class picard.sam.ViewSam
-
- IntervalListScatterer - Class in picard.util
-
- IntervalListScatterer(IntervalListScatterer.Mode) - Constructor for class picard.util.IntervalListScatterer
-
- IntervalListScatterer.Mode - Enum in picard.util
-
- IntervalListToBed - Class in picard.util
-
Trivially simple command line program to convert an IntervalList file to a BED file.
- IntervalListToBed() - Constructor for class picard.util.IntervalListToBed
-
- IntervalListTools - Class in picard.util
-
Little class to aid working with interval lists.
- IntervalListTools() - Constructor for class picard.util.IntervalListTools
-
- IntervalListTools.Action - Enum in picard.util
-
- INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- INTERVALS - Variable in class picard.analysis.CollectMultipleMetrics
-
- INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
-
- INTERVALS - Variable in class picard.analysis.CollectWgsMetrics
-
- INTERVALS - Variable in class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
- Intervals - Class in picard.cmdline.programgroups
-
- Intervals() - Constructor for class picard.cmdline.programgroups.Intervals
-
- INTERVALS - Variable in class picard.reference.NonNFastaSize
-
- INTERVALS - Variable in class picard.sam.MergeSamFiles
-
- INTERVALS - Variable in class picard.vcf.GenotypeConcordance
-
- INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary aligments that align to an intronic base for some gene, and not a coding or UTR base.
- INVERT - Variable in class picard.util.IntervalListTools
-
- IO_SIZE - Variable in class picard.util.FifoBuffer
-
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
-
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.SetNmAndUqTags
-
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
-
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
-
- IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
-
- isAdapterSequence(byte[]) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns
true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isBlank(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
-
- isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
-
- isClosed() - Method in class picard.util.CircularByteBuffer
-
Returns true if the buffer is closed, false otherwise.
- isComment(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isContaminant(HitsForInsert) - Method in class picard.sam.AbstractAlignmentMerger
-
- isContaminant(HitsForInsert) - Method in class picard.sam.SamAlignmentMerger
-
Criteria for contaminant reads:
1.
- isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
-
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
- isDelimiter(byte) - Method in class picard.util.AbstractInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.CsvInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.TabbedInputParser
-
Determines whether a given character is a delimiter
- isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
-
- isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
-
- isHeterozygous() - Method in enum picard.fingerprint.DiploidGenotype
-
- isHomomozygous() - Method in enum picard.fingerprint.DiploidGenotype
-
- isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
-
- isMetricsClass(ClassDoc) - Static method in class picard.util.MetricsDoclet
-
Checks to see if the class extends MetricBase using only the JavaDoc
metadata provided about the class.
- isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is MISSING.
- isOpticalDuplicate - Variable in class picard.sam.markduplicates.util.ReadEnds
-
A *transient* flag marking this read end as being an optical duplicate.
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
-
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- isPf() - Method in class picard.illumina.parser.ClusterData
-
- isPhasing(IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
-
- isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
-
- isSkipBlankLines() - Method in class picard.util.AbstractInputParser
-
- isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
-
- isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
-
- isUsableSnp(VariantContext) - Static method in class picard.fingerprint.FingerprintChecker
-
Quick method to check and see if the variant context represents a usable SNP variant.
- isValidBase(byte) - Static method in enum picard.fingerprint.DiploidGenotype
-
- isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is a VAR.
- iterator() - Method in class picard.annotation.Gene
-
- iterator() - Method in class picard.illumina.parser.IlluminaDataProvider
-
- iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
- iterator() - Method in class picard.illumina.parser.TileIndex
-
- iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
-
- iterator() - Method in class picard.util.AbstractInputParser
-
- iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Creates the iterator object.
- Iterators - Class in picard.util
-
- Iterators() - Constructor for class picard.util.Iterators
-
- iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
-
Renders the embodied regions of the VCF files in the form of CloseableIterators over
VariantContexts.
- MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- MAD_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The median absolute deviation of coverage of the genome after all filters are applied.
- main(String[]) - Static method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- main(String[]) - Static method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
-
- main(String[]) - Static method in class picard.analysis.CollectAlignmentSummaryMetrics
-
Required main method implementation.
- main(String[]) - Static method in class picard.analysis.CollectBaseDistributionByCycle
-
- main(String[]) - Static method in class picard.analysis.CollectGcBiasMetrics
-
- main(String[]) - Static method in class picard.analysis.CollectInsertSizeMetrics
-
Required main method implementation.
- main(String[]) - Static method in class picard.analysis.CollectJumpingLibraryMetrics
-
Stock main method.
- main(String[]) - Static method in class picard.analysis.CollectMultipleMetrics
-
- main(String[]) - Static method in class picard.analysis.CollectOxoGMetrics
-
- main(String[]) - Static method in class picard.analysis.CollectRnaSeqMetrics
-
Required main method implementation.
- main(String[]) - Static method in class picard.analysis.CollectRrbsMetrics
-
- main(String[]) - Static method in class picard.analysis.CollectWgsMetrics
-
- main(String[]) - Static method in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- main(String[]) - Static method in class picard.analysis.CollectWgsMetricsFromSampledSites
-
Deprecated.
- main(String[]) - Static method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
-
- main(String[]) - Static method in class picard.analysis.CompareMetrics
-
- main(String[]) - Static method in class picard.analysis.directed.CollectHsMetrics
-
Stock main method.
- main(String[]) - Static method in class picard.analysis.directed.CollectTargetedPcrMetrics
-
Stock main method.
- main(String[]) - Static method in class picard.analysis.MeanQualityByCycle
-
Required main method.
- main(String[]) - Static method in class picard.analysis.QualityScoreDistribution
-
Required main method.
- main(String[]) - Static method in class picard.cmdline.CreateHtmlDocForProgram
-
- main(String[]) - Static method in class picard.cmdline.CreateHtmlDocForStandardOptions
-
- main(String[]) - Static method in class picard.cmdline.PicardCommandLine
-
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
- main(String[]) - Static method in class picard.fastq.BamToBfq
-
- main(String[]) - Static method in class picard.fingerprint.CheckFingerprint
-
- main(String[]) - Static method in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Stock main method.
- main(String[]) - Static method in class picard.illumina.CheckIlluminaDirectory
-
Required main method implementation.
- main(String[]) - Static method in class picard.illumina.CollectIlluminaBasecallingMetrics
-
- main(String[]) - Static method in class picard.illumina.CollectIlluminaLaneMetrics
-
- main(String[]) - Static method in class picard.illumina.ExtractIlluminaBarcodes
-
- main(String[]) - Static method in class picard.illumina.IlluminaBasecallsToFastq
-
- main(String[]) - Static method in class picard.illumina.IlluminaBasecallsToSam
-
- main(String[]) - Static method in class picard.illumina.MarkIlluminaAdapters
-
- main(String[]) - Static method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
-
Stock main method.
- main(String[]) - Static method in class picard.reference.ExtractSequences
-
- main(String[]) - Static method in class picard.reference.NonNFastaSize
-
- main(String[]) - Static method in class picard.reference.NormalizeFasta
-
- main(String[]) - Static method in class picard.sam.AddCommentsToBam
-
- main(String[]) - Static method in class picard.sam.AddOrReplaceReadGroups
-
Required main method implementation.
- main(String[]) - Static method in class picard.sam.BamIndexStats
-
Stock main method for a command line program.
- main(String[]) - Static method in class picard.sam.BuildBamIndex
-
Stock main method for a command line program.
- main(String[]) - Static method in class picard.sam.CalculateReadGroupChecksum
-
- main(String[]) - Static method in class picard.sam.CheckTerminatorBlock
-
- main(String[]) - Static method in class picard.sam.CleanSam
-
- main(String[]) - Static method in class picard.sam.CompareSAMs
-
- main(String[]) - Static method in class picard.sam.CreateSequenceDictionary
-
- main(String[]) - Static method in class picard.sam.DownsampleSam
-
- main(String[]) - Static method in class picard.sam.DuplicationMetrics
-
- main(String[]) - Static method in class picard.sam.FastqToSam
-
Stock main method.
- main(String[]) - Static method in class picard.sam.FilterSamReads
-
Stock main method.
- main(String[]) - Static method in class picard.sam.FixMateInformation
-
- main(String[]) - Static method in class picard.sam.GatherBamFiles
-
- main(String[]) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
Stock main method.
- main(String[]) - Static method in class picard.sam.markduplicates.MarkDuplicates
-
Stock main method.
- main(String[]) - Static method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
-
Stock main method.
- main(String[]) - Static method in class picard.sam.MergeBamAlignment
-
Required main method implementation.
- main(String[]) - Static method in class picard.sam.MergeSamFiles
-
Required main method implementation.
- main(String[]) - Static method in class picard.sam.PositionBasedDownsampleSam
-
- main(String[]) - Static method in class picard.sam.ReorderSam
-
Required main method implementation.
- main(String[]) - Static method in class picard.sam.ReplaceSamHeader
-
- main(String[]) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
Default main method impl.
- main(String[]) - Static method in class picard.sam.RevertSam
-
Default main method impl.
- main(String[]) - Static method in class picard.sam.SamFormatConverter
-
- main(String[]) - Static method in class picard.sam.SamToFastq
-
- main(String[]) - Static method in class picard.sam.SetNmAndUqTags
-
- main(String[]) - Static method in class picard.sam.SortSam
-
- main(String[]) - Static method in class picard.sam.SplitSamByLibrary
-
- main(String[]) - Static method in class picard.sam.ValidateSamFile
-
- main(String[]) - Static method in class picard.sam.ViewSam
-
- main(String[]) - Static method in class picard.Test
-
- main(String[]) - Static method in class picard.util.BaitDesigner
-
Stock main method.
- main(String[]) - Static method in class picard.util.BedToIntervalList
-
- main(String[]) - Static method in class picard.util.FifoBuffer
-
- main(String[]) - Static method in class picard.util.IntervalListTools
-
- main(String[]) - Static method in class picard.util.LiftOverIntervalList
-
- main(String[]) - Static method in class picard.util.ScatterIntervalsByNs
-
- main(String[]) - Static method in class picard.vcf.CollectVariantCallingMetrics
-
- main(String[]) - Static method in class picard.vcf.filter.FilterVcf
-
- main(String[]) - Static method in class picard.vcf.GatherVcfs
-
- main(String[]) - Static method in class picard.vcf.GenotypeConcordance
-
- main(String[]) - Static method in class picard.vcf.LiftoverVcf
-
- main(String[]) - Static method in class picard.vcf.MakeSitesOnlyVcf
-
- main(String[]) - Static method in class picard.vcf.MergeVcfs
-
- main(String[]) - Static method in class picard.vcf.RenameSampleInVcf
-
- main(String[]) - Static method in class picard.vcf.SortVcf
-
- main(String[]) - Static method in class picard.vcf.SplitVcfs
-
- main(String[]) - Static method in class picard.vcf.UpdateVcfSequenceDictionary
-
- main(String[]) - Static method in class picard.vcf.VcfFormatConverter
-
- main(String[]) - Static method in class picard.vcf.VcfToIntervalList
-
- makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
-
- makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
-
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
-
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
-
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
-
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
-
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
-
- makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
-
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
-
Make an InsertSizeCollector with the given arguments
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
-
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
-
- makeChildCollector(String, String, String) - Method in class picard.analysis.GcBiasMetricsCollector
-
- makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
-
- makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
-
Construct a PerUnitMetricCollector with the given arguments.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectHsMetrics
-
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedMetrics
-
A factory method for the TargetMetricsCollector to use this time.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
-
- makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) - Method in class picard.illumina.parser.MultiTileBclParser
-
- makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
-
- makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Call this method to create a ClusterData iterator over all clusters for all tiles in ascending numeric order.
- makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Call this method to create a ClusterData iterator over the specified tiles.
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Create a string that will be included in any NoSuchElementException thrown by the next() method
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
-
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
-
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
-
- makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
-
- makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
-
- makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
-
- makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
Handles the FastqToSam execution on the FastqReader(s).
- makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a regex string for finding Lane and Tile given a file extension pattern
- makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
-
- makeOverlapDetector(File, SAMFileHeader, File) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
-
- makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
-
- makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
-
- makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
-
- makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
-
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
- MakeSitesOnlyVcf - Class in picard.vcf
-
Writes out a VCF that contains all the site-level information for all records in the input VCF and no per-sample information.
- MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
-
- makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
-
Factory method for the iterator of each tile
- makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
-
Make an CloseableIterator
based on the given file and fileType specified at construction.
- MarkDuplicates - Class in picard.sam.markduplicates
-
A better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
- MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
-
- MarkDuplicates.DuplicateTaggingPolicy - Enum in picard.sam.markduplicates
-
Enum used to control how duplicates are flagged in the DT optional tag on each read.
- MarkDuplicates.DuplicateType - Enum in picard.sam.markduplicates
-
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
- MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
An even better duplication marking algorithm that handles all cases including clipped
and gapped alignments.
- MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
-
- MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
-
This will iterate through a coordinate sorted SAM file (iterator) and either mark or
remove duplicates as appropriate.
- MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Initializes the mark duplicates iterator.
- MarkIlluminaAdapters - Class in picard.illumina
-
Command line program to mark the location of adapter sequences.
- MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
-
- MarkQueue - Class in picard.sam.markduplicates.util
-
This is the mark queue.
- MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
-
- matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
A pattern that will match files of this type for this lane
- MatchResults - Class in picard.fingerprint
-
Represents the results of a fingerprint comparison between one dataset and a specific
fingerprint file.
- MathUtil - Class in picard.util
-
General math utilities
- MathUtil.LogMath - Class in picard.util
-
A collection of common math operations that work with log values.
- MATRIX_OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- max(double[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- max(long[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
-
- MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching read bases to clippable sequence.
- MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
-
- MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
-
- MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- MAX_FS - Variable in class picard.vcf.filter.FilterVcf
-
- MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
-
- MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The maximum measure insert size by alignment.
- MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
-
- MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
-
- MAX_MISMATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- MAX_NO_CALLS - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
-
- MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
-
- MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
- MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
-
The double value closest to 1 while still being less than 1.
- MAX_Q - Variable in class picard.sam.FastqToSam
-
- MAX_READ_LENGTH - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
-
- MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
-
- MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
- MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
-
If more than this many sequences in SAM file, don't spill to disk because there will not
be enough file handles.
- MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
-
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
-
- maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
-
- mean(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the mean of the provided log values.
- mean(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the mean of an array of doubles.
- MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The mean coverage of all amplicons in the experiment.
- MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
-
The mean coverage of all baits in the experiment.
- MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
-
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
- MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of clusters per tile.
- MEAN_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The mean coverage in bases of the genome territory, after all filters are applied.
- MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Mean coverage of CpG sites
- MEAN_INSERT_SIZE - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The mean insert size, after filters are applied.
- MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The mean insert size of the "core" of the distribution.
- MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean percentage of pf clusters per tile.
- MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of pf clusters per tile.
- MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The mean read length of the set of reads examined.
- MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
-
The mean coverage of targets.
- MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The mean coverage of targets.
- MeanQualityByCycle - Class in picard.analysis
-
Program to generate a data table and chart of mean quality by cycle from a
BAM file.
- MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
-
- median(double...) - Static method in class picard.util.MathUtil
-
Calculate the median of an array of doubles.
- MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 3 prime bias of the 1000 most highly expressed transcripts, where 3 prime bias is calculated per
transcript as: mean coverage of the 3' most 100 bases divided by the mean coverage of the whole transcript.
- MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 5 prime bias of the 1000 most highly expressed transcripts, where 5 prime bias is calculated per
transcript as: mean coverage of the 5' most 100 bases divided by the mean coverage of the whole transcript.
- MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The ratio of coverage at the 5' end of to the 3' end based on the 1000 most highly expressed transcripts.
- MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
The median absolute deviation of the distribution.
- MEDIAN_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The median coverage in bases of the genome territory, after all filters are applied.
- MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Median coverage of CpG sites
- MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
-
The median CV of coverage of the 1000 most highly expressed transcripts.
- MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
- MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
-
The median coverage of targets.
- MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The median coverage of targets.
- merge(MergeableMetricBase) - Method in class picard.analysis.replicates.MergeableMetricBase
-
Merge another metric into this one
- merge(Fingerprint) - Method in class picard.fingerprint.Fingerprint
-
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Merges in the likelihood information from the supplied haplotype probabilities object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Merges information from another haplotype probabilities object for the same haplotype into
this object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
-
- merge(ExtractIlluminaBarcodes.BarcodeMetric) - Method in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
Adds the non-calculated
- merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
Adds the non-calculated fields from the other metric to this one.
- merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
-
- merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
-
- MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
-
- MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
-
- MergeableMetricBase - Class in picard.analysis.replicates
-
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated.
- MergeableMetricBase() - Constructor for class picard.analysis.replicates.MergeableMetricBase
-
- MergeableMetricBase.MergeByAdding - Annotation Type in picard.analysis.replicates
-
- MergeableMetricBase.MergeByAssertEquals - Annotation Type in picard.analysis.replicates
-
- MergeableMetricBase.NoMergingIsDerived - Annotation Type in picard.analysis.replicates
-
- mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
-
Merges the alignment data with the non-aligned records from the source BAM file.
- mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
-
Merges the alignment from the map file with the non-aligned records from the source BAM file.
- MergeBamAlignment - Class in picard.sam
-
A command-line tool to merge BAM/SAM alignment info from a third-party aligner with the data in an
unmapped BAM file, producing a third BAM file that has alignment data and all the additional data
from the unmapped BAM
- MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
-
- mergeFingerprintsBySample(Collection<Fingerprint>) - Static method in class picard.fingerprint.FingerprintChecker
-
Takes a collection of fingerprints and, assuming that they are independent, merged the fingerprints
by samples and totals up the probabilities.
- mergeIfCan(MergeableMetricBase) - Method in class picard.analysis.replicates.MergeableMetricBase
-
Merges another MergableMetricBase if possible
- MergeSamFiles - Class in picard.sam
-
Reads a SAM or BAM file and combines the output to one file
- MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
-
- MergeVcfs - Class in picard.vcf
-
Combines multiple VCF files into a single file.
- MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectInsertSizeMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectMultipleMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
-
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- MetricAccumulationLevel - Enum in picard.analysis
-
For use with Picard metrics programs that may output metrics for multiple levels
of aggregation with an analysis.
- Metrics - Class in picard.cmdline.programgroups
-
- Metrics() - Constructor for class picard.cmdline.programgroups.Metrics
-
- METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
-
- METRICS_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
-
- METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- MetricsDoclet - Class in picard.util
-
Doclet for use with JavaDoc that will find all classes extending MetricBase and
output information about the metrics definitions that go along with the classes.
- MetricsDoclet() - Constructor for class picard.util.MetricsDoclet
-
- metricsFiles - Variable in class picard.analysis.CompareMetrics
-
- min(double[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(int[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(short[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(byte[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- MIN_AB - Variable in class picard.vcf.filter.FilterVcf
-
- MIN_DP - Variable in class picard.vcf.filter.FilterVcf
-
- MIN_DP - Variable in class picard.vcf.GenotypeConcordance
-
- MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
-
- MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
-
- MIN_GROUP_COUNT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The minimum measured insert size.
- MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
-
- MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against.
- MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
-
- MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
-
- MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against in a paired end read
- MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small
negative values and see what happens.
- MIN_Q - Variable in class picard.sam.FastqToSam
-
- MIN_QD - Variable in class picard.vcf.filter.FilterVcf
-
- MIN_UNCLIPPED_BASES - Variable in class picard.sam.MergeBamAlignment
-
- MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
-
- MINIMUM_BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectRawWgsMetrics
-
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
-
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CalculateHsMetrics
-
Deprecated.
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectHsMetrics
-
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- MINIMUM_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
-
- MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
-
- MINIMUM_GQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
-
- MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectRawWgsMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CalculateHsMetrics
-
Deprecated.
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectHsMetrics
-
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- MINIMUM_MQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
-
- MINIMUM_QUALITY - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- MINIMUM_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- MINIMUM_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
-
- MINIMUM_RAW_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- MINIMUM_RAW_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
-
- MINIMUM_USABLE_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- MINIMUM_USABLE_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted
-
Deprecated.
- MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
-
- MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
-
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to
a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create
iterators of different data types over the values of file (starting after the end of the header).
- MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
-
- MODE - Variable in class picard.sam.ValidateSamFile
-
- MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode name for which the metrics were calculated.
- MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode sequence for which the metrics were calculated.
- MOLECULAR_INDEX_BASE_QUALITY_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- MOLECULAR_INDEX_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- molecularBarcode - Variable in class picard.illumina.parser.ReadStructure
-
- MolecularIndex - Static variable in enum picard.illumina.parser.ReadType
-
- MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
For a paired-end aligner that aligns each end independently, select the pair of alignments that result
in the largest insert size.
- MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
-
- MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE> - Class in picard.metrics
-
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
- MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
-
- MultilevelMetrics - Class in picard.metrics
-
- MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
-
- MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- multiply(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculates the product of two arrays of the same length.
- MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
-
- multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
-
- MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
-
- MultiTileBclFileUtil - Class in picard.illumina.parser
-
NextSeq-style bcl's have all tiles for a cycle in a single file.
- MultiTileBclParser - Class in picard.illumina.parser
-
Parse .bcl.bgzf files that contain multiple tiles in a single file.
- MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
-
- MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
For file types for which there is one file per lane, with fixed record size, and all the tiles in it,
so the s_.bci file can be used to figure out where each tile starts and ends.
- MultiTileFilterParser - Class in picard.illumina.parser
-
Read filter file that contains multiple tiles in a single file.
- MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
-
- MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
-
- MultiTileLocsParser - Class in picard.illumina.parser
-
Read locs file that contains multiple tiles in a single file.
- MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
-
- MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract class for files with fixed-length records for multiple tiles, e.g.
- MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser
-
- PADDING - Variable in class picard.util.BaitDesigner
-
- PADDING - Variable in class picard.util.IntervalListTools
-
- PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
-
The pair orientation of the reads in this data category.
- PAIRED_RUN - Variable in class picard.fastq.BamToBfq
-
- PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
-
- PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
-
Deprecated.
- PairedVariantSubContextIterator - Class in picard.vcf
-
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
- PairedVariantSubContextIterator(Iterator<VariantContext>, String, Iterator<VariantContext>, String, SAMSequenceDictionary) - Constructor for class picard.vcf.PairedVariantSubContextIterator
-
- PairedVariantSubContextIterator.VcfTuple - Class in picard.vcf
-
Little class to hold a pair of VariantContexts that are in sync with one another.
- PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
-
- ParameterizedFileUtil - Class in picard.illumina.parser
-
- ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
-
- ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
-
- ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
-
- parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
-
- parseOptions(PrintStream, String[]) - Method in class picard.cmdline.CommandLineParser
-
Parse command-line options, and store values in callerOptions object passed to ctor.
- parseOptionsFile(String, boolean) - Method in class picard.cmdline.CommandLineParser
-
- parseTileMetrics(File, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Returns an unmodifiable collection of tile data read from the provided file.
- PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
The "PASS"ing filter String.
- PCT_100X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
- PCT_10X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
- PCT_15X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
- PCT_1X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
- PCT_20X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
- PCT_25X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
- PCT_30X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
- PCT_40X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
- PCT_50X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
- PCT_5X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
- PCT_60X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
- PCT_70X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
- PCT_80X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
- PCT_90X - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
- PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of PF reads that are unaligned and match to a known adapter sequence right from the
start of the read.
- PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
On+Near Amplicon Bases / PF Bases Aligned.
- PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have
the two ends mapping to different chromosomes.
- PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of chimeric pairs expressed as a percentage of the total of all outward facing pairs,
inward-facing pairs, and chimeric pairs.
- PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
CODING_BASES / PF_ALIGNED_BASES
- PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
- PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
- PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
- PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The percentage of high confidence SNPs in dbSNP
- PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The percentage of high confidence Indels in dbSNP
- PCT_EXC_BASEQ - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were of low base quality (default is < 20).
- PCT_EXC_BASEQ - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of aligned bases that were filtered out because they were of low base quality.
- PCT_EXC_BASEQ - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of aligned bases that were filtered out because they were of low base quality.
- PCT_EXC_CAPPED - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they would have raised coverage above the capped value (default cap = 250x).
- PCT_EXC_DUPE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_DUPE - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_DUPE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_MAPQ - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (default is < 20).
- PCT_EXC_MAPQ - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
- PCT_EXC_MAPQ - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
- PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of aligned bases that were filtered out because they did not align over a target base.
- PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of aligned bases that were filtered out because they did not align over a target base.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_TOTAL - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The total fraction of aligned bases excluded due to all filters.
- PCT_EXC_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
- PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
INTERGENIC_BASES / PF_ALIGNED_BASES
- PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
INTRONIC_BASES / PF_ALIGNED_BASES
- PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs expressed as a percentage of the total of all outward facing pairs,
inward-facing pairs, and chimeric pairs.
- PCT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The percentage of all reads in the lane that matched to this barcode.
- PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
PCT_UTR_BASES + PCT_CODING_BASES
- PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
- PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pairs expressed as a percentage of the total of all outward facing pairs,
inward-facing pairs, and chimeric pairs.
- PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of aligned PF bases that mapped neither on or near an amplicon.
- PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of aligned PF bases that mapped neither on or near a bait.
- PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
- PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
- PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
- PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of PF_READS
- PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
- PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of reads that are PF (PF_READS / TOTAL_READS)
- PCT_PF_READS - Variable in class picard.analysis.directed.HsMetrics
-
PF reads / total reads.
- PCT_PF_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
PF reads / total reads.
- PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of PF reads that aligned to the reference sequence.
- PCT_PF_UQ_READS - Variable in class picard.analysis.directed.HsMetrics
-
PF Unique Reads / Total Reads.
- PCT_PF_UQ_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
PF Unique Reads / Total Reads.
- PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
-
PF Reads Aligned / PF Reads.
- PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
PF Reads Aligned / PF Reads.
- PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of reads whose mate pair was also aligned to the reference.
- PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
RIBOSOMAL_BASES / PF_ALIGNED_BASES
- PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
-
On+Near Bait Bases / PF Bases Aligned.
- PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 100X or greater coverage.
- PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 10X or greater coverage.
- PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of all target bases achieving 10X or greater coverage.
- PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 1X or greater coverage.
- PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of all target bases achieving 1X or greater coverage.
- PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 20X or greater coverage.
- PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of all target bases achieving 20X or greater coverage.
- PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 2X or greater coverage.
- PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of all target bases achieving 2X or greater coverage.
- PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 30X or greater coverage.
- PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The percentage of all target bases achieving 30X or greater coverage.
- PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 40X or greater coverage.
- PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.HsMetrics
-
The percentage of all target bases achieving 50X or greater coverage.
- PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The percentage of bases mapping to mRNA divided by the total number of PF bases.
- PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-bait bases out of the PF bases available.
- PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-target bases out of the PF bases available.
- PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
UTR_BASES / PF_ALIGNED_BASES
- PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
-
- PedFile - Class in picard.pedigree
-
Represents a .ped file of family information as documented here:
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
Stores the information in memory as a map of individualId -> Pedigree information for that individual
- PedFile(boolean) - Constructor for class picard.pedigree.PedFile
-
- PedFile.PedTrio - Class in picard.pedigree
-
- PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
-
Constructs a TRIO that cannot be modified after the fact.
- peek() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the first element in this queue
- PER_BASE_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
-
- PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
-
The percentage of mapped sequence that is marked as duplicate.
- percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
-
Obtains percentage of two Longs
- PERFECT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The number of all reads matching this barcode that matched with 0 errors or no-calls.
- PerTileFileUtil - Class in picard.illumina.parser
-
- PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
-
- PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
-
- PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
- PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
-
- PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
-
- PerTilePerCycleFileUtil - Class in picard.illumina.parser
-
- PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
-
- PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
-
- PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
-
- PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable,ARGTYPE> - Interface in picard.metrics
-
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
- PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Constructor that parses the squashed reference to genome reference file and stores the
information in a map for later use.
- PF_ADAPTER_READS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of PF reads that are unaligned and match to a known adapter sequence right from the
start of the read.
- PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
- PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of aligned PF bases.
- PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all PF reads
- PF_BASES - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The total number of bases, before any filters are applied.
- PF_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
THe number of bases in the SAM or BAM file to be examined
- PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of PF bases including non-aligned reads.
- PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter bases assigned to the index.
- PF_BASES_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
- PF_BASES_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
- PF_CHIMERIC_PAIRS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of PF reads that map outside of a maximum insert size (100kb) or that have
the two ends mapping to different chromosomes.
- PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of PF clusters assigned to the index.
- PF_DUPE_PAIRS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of duplicate read pairs, before any filters are applied.
- PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed empty.
- PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed "misaligned".
- PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed multiclonal.
- PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile.
- PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that have not been classified.
- PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of bases aligned to the reference sequence in reads that were mapped at high
quality.
- PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
- PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence with a mapping quality of
Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the
alignment is wrong.
- PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of bases that mismatch the reference in PF HQ aligned reads.
- PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median number of mismatches versus the reference sequence in reads that were aligned
to the reference at high quality (i.e.
- PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of insertion and deletion events per 100 aligned bases.
- PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
- PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that are marked as noise reads.
- PF_NOISE_READS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of PF reads that are marked as noise reads.
- PF_NORMALIZED_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The "normalized" matches to each barcode.
- PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 1 error or no-call.
- PF_ORIENTED_PAIRS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of read pairs with standard orientations from which to calculate mean insert size, after filters are applied.
- PF_PASSING_BASES - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of passing bases, after all filters are applied.
- PF_PCT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The percentage of PF reads in the lane that matched to this barcode.
- PF_PERFECT_MATCHES - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
- PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 20 or higher
- PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The sum of quality scores of all bases divided by 20
- PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 30 or higher
- PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The rate of PF reads matching this barcode to PF reads matching the most prevelant barcode.
- PF_READ_PAIRS - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of read pairs, before all filters are applied.
- PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads where PF is defined as passing Illumina's filter.
- PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of reads that are PF - pass filter
- PF_READS - Variable in class picard.analysis.directed.HsMetrics
-
The number of reads that pass the vendor's filter.
- PF_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of reads that pass the vendor's filter.
- PF_READS - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The number of PF reads matching this barcode (always less than or equal to READS).
- PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter reads assigned to the index.
- PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence.
- PF_READS_ALIGNED - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
The number of aligned reads, before any filters are applied.
- PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
-
- PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
-
- PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
-
- PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
Tracks the number of read pairs that we see that are PF (used to calculate library size)
- PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
Tracks the number of unique PF reads pairs we see (used to calc library size)
- PF_STATUS - Variable in class picard.sam.ViewSam
-
- PF_UNIQUE_READS - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF reads that are not marked as duplicates.
- PF_UNIQUE_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF reads that are not marked as duplicates.
- PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
-
The number of bases in the PF aligned reads that are mapped to a reference base.
- PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
- PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
- PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
- PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
- PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
This ctor is necessary for when reading metrics from file
- PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
- PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
This ctor is necessary for when reading metrics from file
- PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
-
- pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
The program groups that have been seen during the course of examining the input records.
- PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
- PhysicalLocation - Interface in picard.sam.util
-
Small interface that provides access to the physical location information about a cluster.
- PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
-
Stores the minimal information needed for optical duplicate detection.
- PhysicalLocationForMateCigar(PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
-
This stores records that are comparable for detecting optical duplicates.
- PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
- PhysicalLocationInt - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationInt() - Constructor for class picard.sam.util.PhysicalLocationInt
-
- PhysicalLocationShort - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationShort() - Constructor for class picard.sam.util.PhysicalLocationShort
-
- picard - package picard
-
- picard.analysis - package picard.analysis
-
- picard.analysis.artifacts - package picard.analysis.artifacts
-
- picard.analysis.directed - package picard.analysis.directed
-
- picard.analysis.replicates - package picard.analysis.replicates
-
- picard.annotation - package picard.annotation
-
- picard.cmdline - package picard.cmdline
-
- picard.cmdline.programgroups - package picard.cmdline.programgroups
-
- picard.fastq - package picard.fastq
-
- picard.filter - package picard.filter
-
- picard.fingerprint - package picard.fingerprint
-
- picard.illumina - package picard.illumina
-
- picard.illumina.parser - package picard.illumina.parser
-
- picard.illumina.parser.fakers - package picard.illumina.parser.fakers
-
- picard.illumina.parser.readers - package picard.illumina.parser.readers
-
- picard.illumina.quality - package picard.illumina.quality
-
- picard.metrics - package picard.metrics
-
- picard.pedigree - package picard.pedigree
-
- picard.reference - package picard.reference
-
- picard.sam - package picard.sam
-
- picard.sam.markduplicates - package picard.sam.markduplicates
-
- picard.sam.markduplicates.util - package picard.sam.markduplicates.util
-
- picard.sam.util - package picard.sam.util
-
- picard.util - package picard.util
-
- picard.vcf - package picard.vcf
-
- picard.vcf.filter - package picard.vcf.filter
-
- picard.vcf.processor - package picard.vcf.processor
-
- picard.vcf.processor.util - package picard.vcf.processor.util
-
- PicardCommandLine - Class in picard.cmdline
-
This is the main class of Picard and is the way of executing individual command line programs.
- PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
-
- PicardException - Exception in picard
-
Basic Picard runtime exception that, for now, does nothing much
- PicardException(String) - Constructor for exception picard.PicardException
-
- PicardException(String, Throwable) - Constructor for exception picard.PicardException
-
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
-
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
-
- pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
-
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
- PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- PLATFORM - Variable in class picard.sam.FastqToSam
-
- PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
-
- PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
-
- pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities
that sum to 1 with as much fidelity as possible.
- pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
-
Takes a vector of numbers and converts it to a vector of probabilities
that sum to 1 with as much fidelity as possible.
- poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
-
The poll method will return the read end that is *not* the duplicate of all comparable read ends that
have been seen.
- POOL_SIZE - Variable in class picard.util.BaitDesigner
-
- PosFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
-
- PosFileReader - Class in picard.illumina.parser.readers
-
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
-
- POSITION - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The position of the SNP on the chromosome.
- POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Position within the sequence of the CpG site
- PositionalArguments - Annotation Type in picard.cmdline
-
Used to annotate which field of a CommandLineProgram should store parameters given at the
command line which are not options.
- PositionBasedDownsampleSam - Class in picard.sam
-
Class to downsample a BAM file while respecting that we should either get rid
of both ends of a pair or neither end of the pair.
- PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
-
- PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
- PosParser - Class in picard.illumina.parser
-
PosParser parses multiple files formatted as one of the three file formats that contain position information
only (pos, locs, and clocs).
- PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
-
- PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
-
- Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the PPV defined by the scheme across the subset of call states.
- PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
-
- PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
-
- PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
- PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
- PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
-
Performs on-the-fly filtering of the provided VariantContext Iterator such that only variants that satisfy
all predicates are emitted.
- PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
-
- PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
-
- PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
- PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
-
- PrimaryAlignmentSelectionStrategy - Interface in picard.sam
-
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever
strategy is appropriate.
- printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
-
When a command does not match any known command, searches for similar commands, using the same method as GIT
- PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
-
- PROBABILITY - Variable in class picard.sam.DownsampleSam
-
- process() - Method in class picard.vcf.processor.VariantProcessor
-
- product(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
-
- PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
-
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
-
- PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
-
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
-
- PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
-
- PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- promote(int[]) - Static method in class picard.util.MathUtil
-
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
- proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
-
- PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
-
- pSameAlleleWhenMismatchingUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- pSameUmiInIndependentBiDup - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
-
- put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Store the element in the map with the given key.
- R - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- RANDOM_SEED - Variable in class picard.sam.DownsampleSam
-
- randomSublist(List<T>, int) - Static method in class picard.fingerprint.FingerprintChecker
-
A small utility function to choose n random elements (un-shuffled) from a list
- Range - Class in picard.illumina.parser
-
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
- Range(int, int) - Constructor for class picard.illumina.parser.Range
-
- rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParser
-
Very specialized method to rapidly parse a sequence of digits from a String up until the first
non-digit character.
- RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The rate of all reads matching this barcode to all reads matching the most prevelant barcode.
- RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
-
- RE_REVERSE - Variable in class picard.sam.SamToFastq
-
- read(File) - Method in class picard.fingerprint.GenotypeReader
-
- read(File, IntervalList) - Method in class picard.fingerprint.GenotypeReader
-
- read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
-
Read bytes from the buffer into the supplied array.
- read1 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
-
- READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
-
- READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
-
- READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
-
- READ1_TRIM - Variable in class picard.sam.SamToFastq
-
- read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
-
- read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
-
- read2 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
-
- READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
-
- READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
-
- READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
-
- READ2_TRIM - Variable in class picard.sam.SamToFastq
-
- read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
-
- read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
-
- READ_CHUNK_SIZE - Variable in class picard.fastq.BamToBfq
-
- READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
-
- READ_GROUP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The sequencing read group from which sequence data was fingerprinted.
- READ_GROUP - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The read group from which sequence data was drawn for comparison.
- READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
-
The read group to which these metrics apply.
- READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
-
- READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The average read length of all the reads (will be fixed for a lane)
- READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
-
- READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- READ_NAME_PREFIX - Variable in class picard.fastq.BamToBfq
-
- READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
-
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs that were marked as duplicates.
- READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs duplicates that were caused by optical duplication.
- READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
-
The total number of read pairs that were examined in the entire distribution.
- READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
-
The number of mapped read pairs examined.
- READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
-
The number of reads whose start position is at the start of a window of this GC.
- READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
-
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
-
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
-
- READ_STRUCTURE - Variable in class picard.illumina.ExtractIlluminaBarcodes
-
- READ_STRUCTURE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- READ_STRUCTURE - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
-
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
-
Heart of CLP.
- readCount - Variable in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
- ReadData - Class in picard.illumina.parser
-
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
- ReadData() - Constructor for class picard.illumina.parser.ReadData
-
- ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
-
- ReadDescriptor - Class in picard.illumina.parser
-
Represents one set of cycles in an ReadStructure (e.g.
- ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
-
- ReadEnds - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
- ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
-
- ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
- ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
-
Codec for ReadEnds that just outputs the primitive fields and reads them back.
- ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
-
Interface for storing and retrieving ReadEnds objects.
- ReadEndsForMarkDuplicatesWithBarcodes - Class in picard.sam.markduplicates.util
-
- ReadEndsForMarkDuplicatesWithBarcodes() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- ReadEndsForMarkDuplicatesWithBarcodesCodec - Class in picard.sam.markduplicates.util
-
Created by nhomer on 9/13/15.
- ReadEndsForMarkDuplicatesWithBarcodesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
-
- ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
-
A class to store individual records for MarkDuplicatesWithMateCigar.
- ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Builds a read ends object that represents a single read.
- ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Creates a shallow copy from the "other"
- readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
-
- readLaneTiles(File, ReadStructure) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
- readLengths - Variable in class picard.illumina.parser.ReadStructure
-
- ReadNameEncoder - Interface in picard.fastq
-
- ReadNameParser - Class in picard.sam.util
-
Provides access to the physical location information about a cluster.
- ReadNameParser() - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the default read name regex and optical duplicate distance.
- ReadNameParser(String) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- ReadNameParser(String, Log) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- readNextLine() - Method in class picard.util.AbstractInputParser
-
- readNextLine() - Method in class picard.util.BasicInputParser
-
Workhorse method that reads the next line from the underlying reader
- readOneBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- ReadPair() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
-
- READS - Variable in class picard.illumina.ExtractIlluminaBarcodes.BarcodeMetric
-
The total number of reads matching the barcode.
- READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The total number of reads examined
- READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of mapped reads processed
- READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of aligned reads whose mate pair was also aligned to the reference.
- READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for exceeding the mismatch threshold
- READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded due to being too short
- READS_TO_ALIGN - Variable in class picard.fastq.BamToBfq
-
- READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for having no CpG sites
- ReadStructure - Class in picard.illumina.parser
-
Describes the intended logical output structure of clusters of an Illumina run.
- ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
-
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
- ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
-
Converts readStructureString into a List and calls the primary constructor using this List as it's argument.
- ReadStructure.Substructure - Class in picard.illumina.parser
-
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous
in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
- readTwoBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
-
- ReadType - Enum in picard.illumina.parser
-
A read type describes a stretch of cycles in an ReadStructure
(e.g.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingDuplicateFilter
-
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingFilter
-
Return true if we are to filter this record out, false otherwise.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingMapQFilter
-
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingPairedFilter
-
- RECORDS_ONLY - Variable in class picard.sam.ViewSam
-
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as C in read 1 and G in read 2.
- REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as G in read 1 and C in read 2.
- REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of reference alleles observed
- REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics
-
- REFERENCE - Variable in class picard.sam.CreateSequenceDictionary
-
- REFERENCE - Variable in class picard.sam.ReorderSam
-
- REFERENCE - Variable in class picard.util.ScatterIntervalsByNs
-
- REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
-
- REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectOxoGMetrics
-
- REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectWgsMetrics
-
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
-
- REFERENCE_SEQUENCE - Variable in class picard.reference.ExtractSequences
-
- REFERENCE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
-
- REFERENCE_SEQUENCE - Variable in class picard.util.BaitDesigner
-
- REFERENCE_SEQUENCE - Variable in class picard.vcf.LiftoverVcf
-
- REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
-
- RefFlatReader - Class in picard.annotation
-
Loads gene annotations from a refFlat file into an OverlapDetector.
- RefFlatReader.RefFlatColumns - Enum in picard.annotation
-
- reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics
to the outputMetrics' attributes of the same name.
- REJECT - Variable in class picard.vcf.LiftoverVcf
-
- remove() - Method in class picard.illumina.parser.IlluminaDataProvider
-
- remove() - Method in class picard.illumina.parser.MultiTileParser
-
- remove() - Method in class picard.illumina.parser.PerTileParser
-
- remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
- remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
-
- remove() - Method in class picard.illumina.parser.readers.BclReader
-
- remove() - Method in class picard.illumina.parser.readers.FilterFileReader
-
- remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
-
- remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
- remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
-
- remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Removes the end from this set, if present
- remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Remove element with given key from the map.
- remove() - Method in class picard.util.AsyncIterator
-
- remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
-
- remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
-
- remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
-
- remove() - Method in class picard.vcf.PairedVariantSubContextIterator
-
- remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
-
- REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
-
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
-
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
-
- REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
- REMOVE_SEQUENCING_DUPLICATES - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- removeIncompleteTrios() - Method in class picard.pedigree.PedFile
-
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
- removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- RenameSampleInVcf - Class in picard.vcf
-
- RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
-
- renderTileMetricsFileFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Returns the path to the TileMetrics file given the basecalling directory.
- ReorderSam - Class in picard.sam
-
Reorders a SAM/BAM input file according to the order of contigs in a second reference sequence
- ReorderSam() - Constructor for class picard.sam.ReorderSam
-
- REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
-
- replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Replaces a given end with the other end.
- ReplaceSamHeader - Class in picard.sam
-
- ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
-
- replicationRateFromReplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
-
- resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
-
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
-
- result() - Method in class picard.vcf.CallingMetricAccumulator
-
- result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
-
- REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
- REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
- REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
- RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
-
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs.
- RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
- RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum in picard.sam
-
Used as a return for the canSkipSAMFile function.
- RevertSam - Class in picard.sam
-
Reverts a SAM file by optionally restoring original quality scores and by removing
all alignment information.
- RevertSam() - Constructor for class picard.sam.RevertSam
-
- revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
-
Takes an individual SAMRecord and applies the set of changes/reversions to it that
have been requested by program level options.
- reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is
low.
- RExecutor - Class in picard.util
-
Util class for executing R scripts.
- RExecutor() - Constructor for class picard.util.RExecutor
-
- RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- RG_TAG - Variable in class picard.sam.SamToFastq
-
- RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGID - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
-
- RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary aligments that align to ribosomal sequence.
- RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
-
- rightVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
-
- RnaSeqMetrics - Class in picard.analysis
-
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics
program and usually stored in a file with the extension ".rna_metrics".
- RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
-
- RnaSeqMetricsCollector - Class in picard.analysis.directed
-
- RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
-
- RnaSeqMetricsCollector.StrandSpecificity - Enum in picard.analysis.directed
-
- round(double, int) - Static method in class picard.util.MathUtil
-
Round off the value to the specified precision.
- RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
-
- RrbsCpgDetailMetrics - Class in picard.analysis
-
Holds information about CpG sites encountered for RRBS processing QC
- RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
-
- RrbsMetricsCollector - Class in picard.analysis
-
- RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
-
- RrbsSummaryMetrics - Class in picard.analysis
-
Holds summary statistics from RRBS processing QC
- RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
-
- RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- run() - Method in class picard.Test
-
- RUN_BARCODE - Variable in class picard.fastq.BamToBfq
-
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- RUN_DATE - Variable in class picard.sam.FastqToSam
-
- RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
-
- RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- SamAlignmentMerger - Class in picard.sam
-
Class that takes in a set of alignment information in SAM format and merges it with the set
of all reads for which alignment was attempted, stored in an unmapped SAM file.
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int) - Constructor for class picard.sam.SamAlignmentMerger
-
Constructor
- samFiles - Variable in class picard.sam.CompareSAMs
-
- SamFormatConverter - Class in picard.sam
-
Converts a BAM file to human-readable SAM output or vice versa
- SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
-
- SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
-
- SamOrBam - Class in picard.cmdline.programgroups
-
- SamOrBam() - Constructor for class picard.cmdline.programgroups.SamOrBam
-
- SAMPLE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of the sample who's genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The sample whose known genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- SAMPLE - Variable in class picard.metrics.MultilevelMetrics
-
The sample to which these metrics apply.
- SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
-
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
-
- SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
-
- SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The name of the sample being assayed
- SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- SAMPLE_NAME - Variable in class picard.sam.FastqToSam
-
- SAMPLE_SIZE - Variable in class picard.analysis.CollectWgsMetrics
-
- SAMPLE_SIZE - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- sampleBarcodes - Variable in class picard.illumina.parser.ReadStructure
-
- sampleCumulativeSums(int, int, boolean) - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
-
- SampledWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetricsFromSampledSites.SampledWgsMetrics
-
Deprecated.
- SAMRecordAndReference - Class in picard.metrics
-
- SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
-
- SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> - Class in picard.metrics
-
- SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
-
- SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> - Class in picard.metrics
-
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
- SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
-
- samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
-
This class sets the duplicate read flag as the result state when examining sets of records.
- SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
-
- SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
-
- SamToFastq - Class in picard.sam
-
Extracts read sequences and qualities from the input SAM/BAM file and writes them into
the output file in Sanger fastq format.
- SamToFastq() - Constructor for class picard.sam.SamToFastq
-
- SANITIZE - Variable in class picard.sam.RevertSam
-
- scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
-
This function returns the scaled probability of the evidence collected
given a vector of priors on the haplotype using the internal likelihood, which may be
scaled by an unknown factor.
- SCAN_WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
-
- scanDir(File, String) - Method in class picard.cmdline.ClassFinder
-
Scans a directory on the filesystem for classes.
- scanJar(File, String) - Method in class picard.cmdline.ClassFinder
-
Scans the entries in a ZIP/JAR file for classes under the parent package.
- scatter(IntervalList, int) - Method in class picard.util.IntervalListScatterer
-
- scatter(IntervalList, int, boolean) - Method in class picard.util.IntervalListScatterer
-
- SCATTER_COUNT - Variable in class picard.util.IntervalListTools
-
- ScatterIntervalsByNs - Class in picard.util
-
A CLP for breaking up a reference into intervals of Ns and ACGTs bases.
- ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
-
- scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
-
The underlying scheme
- score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- SCORE - Variable in class picard.util.IntervalListToBed
-
- SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation of clusters per tile.
- SD_COVERAGE - Variable in class picard.analysis.CollectWgsMetrics.WgsMetrics
-
The standard deviation of coverage of the genome after all filters are applied.
- SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in percentage of pf clusters per tile.
- SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in number of pf clusters per tile.
- SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
-
- SECOND_INPUT - Variable in class picard.util.IntervalListTools
-
- SECONDARY_OR_SUPPLEMENTARY_RDS - Variable in class picard.sam.DuplicationMetrics
-
The number of reads that were either secondary or supplementary
- seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
-
- seekToTile(int) - Method in class picard.illumina.parser.IlluminaDataProvider
-
Jump so that the next record returned will be from the specified tile.
- seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
-
- seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
-
- seq(double, double, double) - Static method in class picard.util.MathUtil
-
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
- SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
-
- SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
-
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
-
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
-
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
-
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
-
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
-
- SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Sequence the CpG is seen in
- SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
-
- SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
-
- SequencingArtifactMetrics - Class in picard.analysis.artifacts
-
- SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
-
- SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
-
Bait bias artifacts broken down by context.
- SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
- SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
-
Pre-adapter artifacts broken down by context.
- SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single pre-adapter artifact.
- setAllowDuplicateReads(boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
- setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
- setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the name of the bait set explicitly instead of inferring it from the bait file.
- setBases(byte[]) - Method in class picard.illumina.parser.ReadData
-
- setBigDuplicateSetSize(int) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Sets the size of a set that is big enough to log progress about.
- setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
- setConverter(IlluminaBasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.IlluminaBasecallsConverter
-
Must be called before doTileProcessing.
- setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
-
- setGenotypingErrorRate(double) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the assumed genotyping error rate used when accurate error rates are not available.
- setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
- setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
- setLane(int) - Method in class picard.illumina.parser.ClusterData
-
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
-
- setLibraryId(short) - Method in interface picard.sam.util.PhysicalLocation
-
- setLibraryId(short) - Method in class picard.sam.util.PhysicalLocationInt
-
- setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
- setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
-
- setmaximalPLDifference(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the maximal difference in PL scores considered when reading PLs from a VCF.
- setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
-
- setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
-
Allows the caller to override the maximum records in RAM.
- setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
-
- setMessageStream(PrintStream) - Method in class picard.cmdline.CommandLineParser
-
This method is only needed when calling one of the public methods that doesn't take a messageStream argument.
- setMinimumBaseQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
- setMinimumMappingQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
- setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
-
- setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
-
- setNearProbeDistance(int) - Method in class picard.analysis.directed.TargetMetricsCollector
-
Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- SetNmAndUqTags - Class in picard.sam
-
- SetNmAndUqTags() - Constructor for class picard.sam.SetNmAndUqTags
-
- setNoise(FourChannelIntensityData) - Method in class picard.illumina.parser.ReadData
-
- setNoSideEffects(boolean) - Method in class picard.analysis.directed.TargetMetricsCollector
-
In the case of ignoring bases in overlapping reads from the same template,
we choose to internally modify the SAM record's CIGAR to clip overlapping bases.
- setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
- setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
-
- setPerBaseOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-base coverage information to.
- setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-target coverage information to.
- setPf(boolean) - Method in class picard.illumina.parser.ClusterData
-
- setpLossofHet(double) - Method in class picard.fingerprint.FingerprintChecker
-
- setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
-
- setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
-
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones
available via enum.
- setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
-
- setRawIntensities(FourChannelIntensityData) - Method in class picard.illumina.parser.ReadData
-
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
-
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
-
- setReadGroup(short) - Method in interface picard.sam.util.PhysicalLocation
-
- setReadGroup(short) - Method in class picard.sam.util.PhysicalLocationInt
-
- setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
-
- setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
-
- setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
-
- setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
When this number of adapters have been matched, discard the least-frequently matching ones.
- setTile(int) - Method in class picard.illumina.parser.ClusterData
-
- setTile(short) - Method in interface picard.sam.util.PhysicalLocation
-
- setTile(short) - Method in class picard.sam.util.PhysicalLocationInt
-
- setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
- setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectQualityYieldMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
-
- setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time initialization work.
- setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
-
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
- setup(VCFHeader) - Method in class picard.vcf.CallingMetricAccumulator
-
- setup(VCFHeader) - Method in class picard.vcf.GvcfMetricAccumulator
-
- setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
-
- setValuesFromAlignment(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the values from the alignment record on the unaligned BAM record.
- setWordCount(int) - Method in class picard.util.AbstractInputParser
-
- setX(int) - Method in class picard.illumina.parser.ClusterData
-
- setX(int) - Method in interface picard.sam.util.PhysicalLocation
-
- setX(int) - Method in class picard.sam.util.PhysicalLocationInt
-
- setX(int) - Method in class picard.sam.util.PhysicalLocationShort
-
- setY(int) - Method in class picard.illumina.parser.ClusterData
-
- setY(int) - Method in interface picard.sam.util.PhysicalLocation
-
- setY(int) - Method in class picard.sam.util.PhysicalLocationInt
-
- setY(int) - Method in class picard.sam.util.PhysicalLocationShort
-
- Sex - Enum in picard.pedigree
-
Represents the sex of an individual.
- shiftedLogEvidenceProbability() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by
the internal haplotypeFrequencies
- shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
returns the log-probability the evidence, using as priors the posteriors of another object
- shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
-
- shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns true if we should track this for optical duplicate detection, false otherwise
- SinglePassSamProgram - Class in picard.analysis
-
Super class that is designed to provide some consistent structure between subclasses that
simply iterate once over a coordinate sorted BAM and collect information from the records
as the go in order to produce some kind of output.
- SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
-
- SingleTestUnitTest() - Constructor for class picard.util.TestNGUtil.SingleTestUnitTest
-
- size() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the number of SNPs within the haplotype block.
- size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
-
- size() - Method in class picard.sam.markduplicates.util.MarkQueue
-
The number of records currently in this queue.
- size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
The number of records in this set
- size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
- SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
- sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
-
- sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
- Skip - Static variable in enum picard.illumina.parser.ReadType
-
- skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
- skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
-
- skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
-
- skips - Variable in class picard.illumina.parser.ReadStructure
-
- SNP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of a representative SNP within the haplotype that was compared.
- Snp - Class in picard.fingerprint
-
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
- Snp(String, String, int, byte, byte, double, List<String>) - Constructor for class picard.fingerprint.Snp
-
- SNP_ALLELES - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The possible alleles for the SNP.
- SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
-
- SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
- snpCounter - Variable in class picard.vcf.GenotypeConcordance
-
- snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
-
- SORT - Variable in class picard.util.BedToIntervalList
-
- SORT - Variable in class picard.util.IntervalListToBed
-
- SORT - Variable in class picard.util.IntervalListTools
-
- SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
-
- SORT_ORDER - Variable in class picard.sam.FastqToSam
-
- SORT_ORDER - Variable in class picard.sam.FilterSamReads
-
- SORT_ORDER - Variable in class picard.sam.FixMateInformation
-
- SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
-
- SORT_ORDER - Variable in class picard.sam.MergeSamFiles
-
- SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
- SORT_ORDER - Variable in class picard.sam.RevertSam
-
- SORT_ORDER - Variable in class picard.sam.SortSam
-
- SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
-
- SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- SortSam - Class in picard.sam
-
- SortSam() - Constructor for class picard.sam.SortSam
-
- SortVcf - Class in picard.vcf
-
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then
by coordinate.
- SortVcf() - Constructor for class picard.vcf.SortVcf
-
- SPECIES - Variable in class picard.sam.CreateSequenceDictionary
-
- split(String, String[], String) - Method in class picard.Test
-
- SplitSamByLibrary - Class in picard.sam
-
Command-line program to split a SAM or BAM file into separate files based on
library name.
- SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
-
- SplitVcfs - Class in picard.vcf
-
Splits the input VCF file into two, one for indels and one for SNPs.
- SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
-
- STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
Standard deviation of insert sizes over the "core" of the distribution.
- StandardOptionDefinitions - Class in picard.cmdline
-
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix)
is the standard long Option name, and the value of the constant is the standard shortName.
- StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
-
- start - Variable in class picard.annotation.Gene.Transcript.Exon
-
- start() - Method in class picard.annotation.Gene.Transcript
-
- start - Variable in class picard.illumina.parser.Range
-
- start(RootDoc) - Static method in class picard.util.MetricsDoclet
-
Entry point called by the javadoc command line tool.
- start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
-
- start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Starts the work of the executor, returning immediately.
- start() - Method in class picard.vcf.processor.VcfFileSegment
-
- stddev(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stop() - Method in class picard.vcf.processor.VcfFileSegment
-
- STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
-
- STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
-
- STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
-
- STOP_AFTER - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
-
- STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
-
- STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads aligned to the positive strand of the genome divided by the number of
PF reads aligned to the genome.
- STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
-
- STRATEGY - Variable in class picard.sam.DownsampleSam
-
- STRICT - Variable in class picard.vcf.SplitVcfs
-
- stringSeqsToString(String[], String) - Static method in class picard.util.IlluminaUtil
-
- STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
-
- SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
-
- Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
-
Indices into the ReadStructure.descriptors for this specific substructure, indices
must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
- sum(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- sum(double[], double[]) - Static method in class picard.util.MathUtil
-
calculates the sum of the arrays as a third array.
- sum(double[]) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array.
- sum(long[], int, int) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array starting with start and ending before stop.
- SUMMARY - Variable in class picard.metrics.GcBiasMetrics
-
- SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
-
- SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
-
- SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
-
- SUMMARY_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
-
- summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
-
- supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
-
- supportedTypes() - Method in class picard.illumina.parser.PosParser
-
- supportsMetricAccumulationLevel() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
-
- TabbedInputParser - Class in picard.util
-
Parser for tab-delimited files
- TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedTextFileWithHeaderParser - Class in picard.util
-
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
- TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
-
- TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
-
- TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
-
- TabbedTextFileWithHeaderParser.Row - Class in picard.util
-
- TAG_PER_MOLECULAR_INDEX - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- TAGGING_POLICY - Variable in class picard.sam.markduplicates.MarkDuplicates
-
- TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
-
- TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
-
- TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
-
- TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
-
- TARGET_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
-
The unique number of target bases in the experiment where target is usually exons etc.
- TARGET_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of unique bases covered by the intervals of all targets that should be covered
- TargetedPcrMetrics - Class in picard.analysis.directed
-
Metrics class for targeted pcr runs such as TSCA runs
- TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
-
- TargetedPcrMetricsCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
-
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
-
- TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection
or Targeted PCR Techniques (TSCA).
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
-
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
-
- TargetMetricsCollector.Coverage - Class in picard.analysis.directed
-
A simple class that is used to store the coverage information about an interval.
- TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
-
Collect the Target Metrics for one unit of "accumulation" (i.e.
- TARGETS - Variable in class picard.util.BaitDesigner
-
- Template - Static variable in enum picard.illumina.parser.ReadType
-
- templates - Variable in class picard.illumina.parser.ReadStructure
-
- Test - Class in picard
-
- Test() - Constructor for class picard.Test
-
- testDoWork() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
-
Silly method that is necessary to give unit test access to call doWork()
- Testing - Class in picard.cmdline.programgroups
-
- Testing() - Constructor for class picard.cmdline.programgroups.Testing
-
- TestNGParameterizable() - Constructor for class picard.util.TestNGUtil.TestNGParameterizable
-
- TestNGUtil - Class in picard.util
-
Small class implementing some utility functions that are useful for test and interfacing with the TestNG framework.
- TestNGUtil() - Constructor for class picard.util.TestNGUtil
-
- TestNGUtil.SingleTestUnitTest<TestClazz extends TestNGUtil.TestNGParameterizable> - Class in picard.util
-
- TestNGUtil.TestNGParameterizable - Class in picard.util
-
Interface for exposing an implementation for converting an object into a Object[] appropriate for positional
parameter-passing as performed by TestNG.
- TheoreticalSensitivity - Class in picard.analysis
-
Created by David Benjamin on 5/13/15.
- TheoreticalSensitivity() - Constructor for class picard.analysis.TheoreticalSensitivity
-
- TheoreticalSensitivity.RouletteWheel - Class in picard.analysis
-
- THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
-
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
-
- tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The tile, which is determined from the file name
- Tile - Class in picard.illumina.parser
-
Represents a tile from TileMetricsOut.bin.
- Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
-
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The Tile that is described by this metric.
- tile - Variable in class picard.sam.util.PhysicalLocationInt
-
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
-
- TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The expected name of the tile metrics output file.
- TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.IlluminaBasecallsConverter
-
A comparator for tile numbers, which are not necessarily ordered by the number's value.
- TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
-
- tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
-
- TileIndex - Class in picard.illumina.parser
-
Load a file containing 8-byte records like this:
tile number: 4-byte int
number of clusters in tile: 4-byte int
Number of records to read is determined by reaching EOF.
- TileIndex.TileIndexRecord - Class in picard.illumina.parser
-
- tileIsSet() - Method in class picard.illumina.parser.ClusterData
-
- tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
-
- TileMetricsOutReader - Class in picard.illumina.parser.readers
-
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
- TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
-
Return a TileMetricsOutReader for the specified file
- TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
-
Helper class which captures the combination of a lane, tile & metric code
- TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
-
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
- TileMetricsUtil - Class in picard.illumina.parser
-
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
- TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
-
- TilePhasingValue - Class in picard.illumina.parser
-
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
- TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
-
- tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
- TileTemplateRead - Enum in picard.illumina.parser
-
Defines the first or second template read for a tile
- TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
-
- TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TN (true negative) count across all variants
- TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- toClassName(String) - Method in class picard.cmdline.ClassFinder
-
Convert a filename to a class name by removing '.class' and converting '/'s to '.'s.
- toCode() - Method in enum picard.pedigree.Sex
-
Returns the code used to encode this sex in a ped/fam file.
- toObjectArray() - Method in class picard.util.TestNGUtil.TestNGParameterizable
-
- toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any
ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
- toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
- toString() - Method in class picard.fingerprint.HaplotypeBlock
-
- toString() - Method in class picard.fingerprint.Snp
-
- toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
-
- toString() - Method in class picard.illumina.parser.ClusterData
-
- toString() - Method in class picard.illumina.parser.Range
-
- toString() - Method in class picard.illumina.parser.ReadDescriptor
-
- toString() - Method in class picard.illumina.parser.ReadStructure
-
Converts this object into a String using rules complementary to the single string constructor above.
- toString() - Method in enum picard.sam.FilterSamReads.Filter
-
- toString() - Method in class picard.vcf.processor.VcfFileSegment
-
- TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of basecalls observed at all sites.
- TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all reads
- TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of bases assigned to the index.
- TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of clusters that were seen in the gc bias calculation.
- TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of clusters assigned to the index.
- TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of high confidence complex Indel calls that were examined
- TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of high confidence Indel calls that were examined
- TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of high confidence multiallelic SNP calls that were examined
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of reads including all PF and non-PF reads.
- TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of reads in the input file
- TOTAL_READS - Variable in class picard.analysis.directed.HsMetrics
-
The total number of reads in the SAM or BAM file examine.
- TOTAL_READS - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The total number of reads in the SAM or BAM file examine.
- TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of reads assigned to the index.
- TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of sites that had at least one base covering them.
- TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was encountered
- TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of high confidence SNPs calls (i.e.
- totalCycles - Variable in class picard.illumina.parser.ReadStructure
-
- TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TP (true positive) count across all variants
- TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
- trackOpticalDuplicates(List<? extends ReadEnds>, ReadEnds, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Looks through the set of reads and identifies how many of the duplicates are
in fact optical duplicates, and stores the data in the instance level histogram.
- Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
-
- transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
-
- transcriptionStart - Variable in class picard.annotation.Gene.Transcript
-
- triSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- triSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
- TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
-
- TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
-
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
-
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'truth' sample
- TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'truth' sample (i.e.
- TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
-
- TruthAndCallStates(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Constructor for class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
-
- truthState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
-
- TYPE - Variable in class picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
-
Deprecated.
Identifier for metrics type
- type - Variable in class picard.illumina.parser.ReadDescriptor
-
- TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
-
- VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
-
- validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Validates that there are no counts for NA states in the underlying scheme
- ValidateSamFile - Class in picard.sam
-
Command line program wrapping SamFileValidator.
- ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
-
- ValidateSamFile.Mode - Enum in picard.sam
-
- validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
-
Check that all cells in the scheme exist.
- VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
-
- valueOf(String) - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.analysis.CollectMultipleMetrics.Program
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.analysis.CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
-
Deprecated.
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.analysis.MetricAccumulationLevel
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.annotation.LocusFunction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.fingerprint.DiploidGenotype
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.fingerprint.DiploidHaplotype
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.IlluminaDataType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.IntensityChannel
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.ReadType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.parser.TileTemplateRead
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.pedigree.Sex
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.FilterSamReads.Filter
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.ValidateSamFile.Mode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.ViewSam.AlignmentStatus
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.sam.ViewSam.PfStatus
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.util.BaitDesigner.DesignStrategy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.util.IntervalListScatterer.Mode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.util.IntervalListTools.Action
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.util.VariantType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.analysis.CollectMultipleMetrics.Program
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.analysis.CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY
-
Deprecated.
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.analysis.MetricAccumulationLevel
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.annotation.LocusFunction
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.fingerprint.DiploidGenotype
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.fingerprint.DiploidHaplotype
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.IlluminaDataType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.IlluminaMetricsCode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.IntensityChannel
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.ReadType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.parser.TileTemplateRead
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.pedigree.Sex
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.FilterSamReads.Filter
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.ValidateSamFile.Mode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.ViewSam.AlignmentStatus
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.sam.ViewSam.PfStatus
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.util.BaitDesigner.DesignStrategy
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.util.IntervalListScatterer.Mode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.util.IntervalListTools.Action
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.util.VariantType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
- VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
- VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The type of the event (i.e.
- VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> - Interface in picard.vcf.processor
-
- VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,R> - Class in picard.vcf.processor
-
- VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
- VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
- VariantFilter - Interface in picard.vcf.filter
-
Interface for classes that can generate filters for VariantContexts.
- VariantIterator(SAMSequenceDictionary, Object) - Constructor for class picard.fingerprint.GenotypeReader.VariantIterator
-
Deprecated.
- VariantIteratorProducer - Class in picard.vcf.processor
-
A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally
an interval list.
- VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
-
- VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor
-
Describes an object that processes variants and produces a result.
- VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
-
Handles VariantContexts, and accumulates their data in some fashion internally.
- VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT> - Interface in picard.vcf.processor
-
- VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,R> - Class in picard.vcf.processor
-
- VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
-
- VariantType - Enum in picard.util
-
Enum to hold the possible types of dbSnps.
- VCF - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
-
- vcf() - Method in class picard.vcf.processor.VcfFileSegment
-
- VcfFileSegment - Class in picard.vcf.processor
-
Describes a segment of a particular VCF file.
- VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
-
- VcfFileSegmentGenerator - Class in picard.vcf.processor
-
- VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
-
- VcfFormatConverter - Class in picard.vcf
-
Converts an ASCII VCF file to a binary BCF or vice versa.
- VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
-
- VcfOrBcf - Class in picard.cmdline.programgroups
-
- VcfOrBcf() - Constructor for class picard.cmdline.programgroups.VcfOrBcf
-
- VcfToIntervalList - Class in picard.vcf
-
Creates an interval list from a VCF
- VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
-
- VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
-
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
-
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
-
expectedCycles are not checked in this implementation.
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any
missing/or malformed files
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
-
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
- verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
-
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
-
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
-
- version - Variable in class picard.illumina.parser.readers.FilterFileReader
-
Version number found in the FilterFile, this should equal 3
- ViewSam - Class in picard.sam
-
Very simple command that just reads a SAM or BAM file and writes out the header
and each records to standard out.
- ViewSam() - Constructor for class picard.sam.ViewSam
-
- ViewSam.AlignmentStatus - Enum in picard.sam
-
- ViewSam.PfStatus - Enum in picard.sam
-