Constant Field Values

Contents

• picard.analysis.*
• picard.cmdline.*
• picard.fingerprint.*
• picard.illumina.*
• picard.metrics.*
• picard.sam.*
• picard.util.*
• picard.vcf.*

picard.analysis.*

picard.analysis.CollectInsertSizeMetrics

Modifier and Type	Constant Field	Value
protected static final java.lang.String	Histogram_R_SCRIPT	"picard/analysis/insertSizeHistogram.R"

picard.analysis.CollectRrbsMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	DETAIL_FILE_EXTENSION	"rrbs_detail_metrics"
public static final java.lang.String	PDF_FILE_EXTENSION	"rrbs_qc.pdf"
public static final java.lang.String	SUMMARY_FILE_EXTENSION	"rrbs_summary_metrics"

picard.analysis.artifacts.SequencingArtifactMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	BAIT_BIAS_DETAILS_EXT	".bait_bias_detail_metrics"
public static final java.lang.String	BAIT_BIAS_SUMMARY_EXT	".bait_bias_summary_metrics"
public static final java.lang.String	ERROR_SUMMARY_EXT	".error_summary_metrics"
public static final java.lang.String	PRE_ADAPTER_DETAILS_EXT	".pre_adapter_detail_metrics"
public static final java.lang.String	PRE_ADAPTER_SUMMARY_EXT	".pre_adapter_summary_metrics"

picard.analysis.directed.TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

Modifier and Type	Constant Field	Value
public static final int	NEAR_PROBE_DISTANCE_DEFAULT	250

picard.cmdline.*

picard.cmdline.StandardOptionDefinitions

Modifier and Type	Constant Field	Value
public static final java.lang.String	ASSUME_SORT_ORDER_SHORT_NAME	"ASO"
public static final java.lang.String	ASSUME_SORTED_SHORT_NAME	"AS"
public static final java.lang.String	EXPECTED_INSERT_SIZE_SHORT_NAME	"INSERT"
public static final java.lang.String	INPUT_SHORT_NAME	"I"
public static final java.lang.String	LANE_SHORT_NAME	"L"
public static final java.lang.String	LIBRARY_NAME_SHORT_NAME	"LIB"
public static final java.lang.String	METRICS_FILE_SHORT_NAME	"M"
public static final java.lang.String	MINIMUM_LOD_SHORT_NAME	"LOD"
public static final java.lang.String	MINIMUM_MAPPING_QUALITY_SHORT_NAME	"MQ"
public static final java.lang.String	OUTPUT_SHORT_NAME	"O"
public static final java.lang.String	PF_READS_ONLY_SHORT_NAME	"PF"
public static final java.lang.String	PROGRAM_RECORD_ID_SHORT_NAME	"PG"
public static final java.lang.String	READ_GROUP_ID_SHORT_NAME	"RG"
public static final java.lang.String	REFERENCE_SHORT_NAME	"R"
public static final java.lang.String	SAMPLE_ALIAS_SHORT_NAME	"ALIAS"
public static final java.lang.String	SEQUENCE_DICTIONARY_SHORT_NAME	"SD"
public static final java.lang.String	SORT_ORDER_SHORT_NAME	"SO"
public static final java.lang.String	USE_ORIGINAL_QUALITIES_SHORT_NAME	"OQ"

picard.fingerprint.*

picard.fingerprint.CheckFingerprint

Modifier and Type	Constant Field	Value
public static final java.lang.String	FINGERPRINT_DETAIL_FILE_SUFFIX	"fingerprinting_detail_metrics"
public static final java.lang.String	FINGERPRINT_SUMMARY_FILE_SUFFIX	"fingerprinting_summary_metrics"

picard.fingerprint.FingerprintChecker

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_GENOTYPING_ERROR_RATE	0.01
public static final int	DEFAULT_MAXIMAL_PL_DIFFERENCE	30
public static final int	DEFAULT_MINIMUM_BASE_QUALITY	20
public static final int	DEFAULT_MINIMUM_MAPPING_QUALITY	10

picard.fingerprint.HaplotypeMap

Modifier and Type	Constant Field	Value
public static final java.lang.String	HET_GENOTYPE_FOR_PHASING	"HetGenotypeForPhasing"
public static final java.lang.String	PHASESET_PREFIX	"PhaseSet"
public static final java.lang.String	SYNTHETIC_PHASESET_PREFIX	"Synthetic"

picard.illumina.*

picard.illumina.IlluminaBasecallsToSam

Modifier and Type	Constant Field	Value
public static final java.lang.String	USAGE	"Generate a SAM or BAM file from data in an Illumina basecalls output directory"

picard.illumina.parser.MultiTileBclParser

Modifier and Type	Constant Field	Value
public static final byte	MASKING_QUALITY	2

picard.illumina.parser.ParameterizedFileUtil

Modifier and Type	Constant Field	Value
protected static final boolean	DefaultSkipEmptyFiles	true
public static final java.lang.String	PER_TILE_PATTERN_STRING	"s_(\\d+)_(\\d{1,5})"

picard.illumina.parser.ReadStructure

Modifier and Type	Constant Field	Value
public static final java.lang.String	PARAMETER_DOC	"A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein."

picard.illumina.parser.readers.AbstractIlluminaPositionFileReader

Modifier and Type	Constant Field	Value
public static final float	MAX_POS	1.0E7f
public static final float	MIN_POS	-10.0f
public static final java.lang.String	S_LOCS_FILE	"s.locs"

picard.illumina.parser.readers.BclQualityEvaluationStrategy

Modifier and Type	Constant Field	Value
public static final int	ILLUMINA_ALLEGED_MINIMUM_QUALITY	2

picard.illumina.parser.readers.FilterFileReader

Modifier and Type	Constant Field	Value
public static final int	EXPECTED_VERSION	3

picard.illumina.quality.CollectHiSeqXPfFailMetrics

Modifier and Type	Constant Field	Value
public static final java.lang.String	detailedMetricsExtension	".pffail_detailed_metrics"
public static final java.lang.String	summaryMetricsExtension	".pffail_summary_metrics"

picard.metrics.*

picard.metrics.MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends java.lang.Comparable,ARGTYPE>

Modifier and Type	Constant Field	Value
public static final java.lang.String	UNKNOWN	"unknown"

picard.sam.*

picard.sam.AbstractAlignmentMerger

Modifier and Type	Constant Field	Value
public static final int	MAX_RECORDS_IN_RAM	500000

picard.sam.SplitSamByLibrary

Modifier and Type	Constant Field	Value
public static final int	NO_LIBRARIES_SPECIFIED_IN_HEADER	2

picard.sam.markduplicates.MarkDuplicates

Modifier and Type	Constant Field	Value
public static final java.lang.String	DUPLICATE_SET_INDEX_TAG	"DI"
public static final java.lang.String	DUPLICATE_SET_SIZE_TAG	"DS"
public static final java.lang.String	DUPLICATE_TYPE_LIBRARY	"LB"
public static final java.lang.String	DUPLICATE_TYPE_SEQUENCING	"SQ"
public static final java.lang.String	DUPLICATE_TYPE_TAG	"DT"

picard.sam.markduplicates.util.OpticalDuplicateFinder

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BIG_DUPLICATE_SET_SIZE	1000
public static final int	DEFAULT_MAX_DUPLICATE_SET_SIZE	300000
public static final int	DEFAULT_OPTICAL_DUPLICATE_DISTANCE	100

picard.sam.markduplicates.util.ReadEnds

Modifier and Type	Constant Field	Value
public static final byte	F	0
public static final byte	FF	2
public static final byte	FR	3
public static final byte	R	1
public static final byte	RF	5
public static final byte	RR	4

picard.sam.markduplicates.util.ReadEndsForMarkDuplicates

Modifier and Type	Constant Field	Value
protected static final int	SIZE_OF	69

picard.sam.util.PhysicalLocation

Modifier and Type	Constant Field	Value
public static final int	NO_VALUE	-1

picard.util.*

picard.util.AdapterMarker

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_ADAPTER_LENGTH	30
public static final int	DEFAULT_NUM_ADAPTERS_TO_KEEP	1
public static final int	DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN	100

picard.util.AsyncIterator<T>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_QUEUE_SIZE	2000

picard.util.ClippingUtility

Modifier and Type	Constant Field	Value
public static final double	MAX_ERROR_RATE	0.1
public static final double	MAX_PE_ERROR_RATE	0.1
public static final int	MIN_MATCH_BASES	12
public static final int	MIN_MATCH_PE_BASES	6
public static final int	NO_MATCH	-1

picard.util.IlluminaUtil

Modifier and Type	Constant Field	Value
public static final java.lang.String	BARCODE_DELIMITER	"-"

picard.util.MathUtil

Modifier and Type	Constant Field	Value
public static final double	MAX_PROB_BELOW_ONE	0.9999999999999999

picard.util.help.HelpConstants

Modifier and Type	Constant Field	Value
public static final java.lang.String	DOC_CAT_FASTA	"Fasta File Tools"
public static final java.lang.String	DOC_CAT_FASTA_SUMMARY	"Tools for analysis and manipulation of files in fasta format"
public static final java.lang.String	DOC_CAT_INTERVALS	"Interval Tools"
public static final java.lang.String	DOC_CAT_INTERVALS_SUMMARY	"Tools for processing intervals and associated overlapping records"
public static final java.lang.String	DOC_CAT_READS	"SAM/BAM/CRAM Tools"
public static final java.lang.String	DOC_CAT_READS_SUMMARY	"Tools for manipulating read-level data (SAM/BAM/CRAM)"
public static final java.lang.String	DOC_CAT_TEST	"Test Tools"
public static final java.lang.String	DOC_CAT_TEST_SUMMARY	"Tools for internal test purposes"
public static final java.lang.String	DOC_CAT_VARIANT	"VCF Tools"
public static final java.lang.String	DOC_CAT_VARIANT_SUMMARY	"Tools for manipulating variants and associated metadata"
public static final java.lang.String	DOC_SUPERCAT_EXCLUDE	"exclude"
public static final java.lang.String	DOC_SUPERCAT_TOOLS	"tools"
public static final java.lang.String	DOC_SUPERCAT_UTILITIES	"utilities"

picard.vcf.*

picard.vcf.GenotypeConcordance

Modifier and Type	Constant Field	Value
public static final java.lang.String	CONTINGENCY_METRICS_FILE_EXTENSION	".genotype_concordance_contingency_metrics"
public static final java.lang.String	CONTINGENCY_STATE_TAG	"CONC_ST"
public static final java.lang.String	DETAILED_METRICS_FILE_EXTENSION	".genotype_concordance_detail_metrics"
public static final java.lang.String	OUTPUT_VCF_CALL_SAMPLE_NAME	"call"
public static final java.lang.String	OUTPUT_VCF_FILE_EXTENSION	".genotype_concordance.vcf.gz"
public static final java.lang.String	OUTPUT_VCF_TRUTH_SAMPLE_NAME	"truth"
public static final java.lang.String	SUMMARY_METRICS_FILE_EXTENSION	".genotype_concordance_summary_metrics"

picard.vcf.LiftoverVcf

Modifier and Type	Constant Field	Value
public static final java.lang.String	ATTEMPTED_LOCUS	"AttemptedLocus"
public static final java.lang.String	FILTER_CANNOT_LIFTOVER_INDEL	"ReverseComplementedIndel"
public static final java.lang.String	FILTER_INDEL_STRADDLES_TWO_INTERVALS	"IndelStraddlesMultipleIntevals"
public static final java.lang.String	FILTER_MISMATCHING_REF_ALLELE	"MismatchedRefAllele"
public static final java.lang.String	FILTER_NO_TARGET	"NoTarget"
public static final java.lang.String	ORIGINAL_CONTIG	"OriginalContig"
public static final java.lang.String	ORIGINAL_START	"OriginalStart"

picard.vcf.filter.AlleleBalanceFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	AB_FILTER	"AlleleBalance"

picard.vcf.filter.FilterApplyingVariantIterator

Modifier and Type	Constant Field	Value
public static final java.lang.String	ALL_GTS_FILTERED	"AllGtsFiltered"
public static final java.lang.String	PASS_FILTER	"PASS"

picard.vcf.filter.QdFilter

Modifier and Type	Constant Field	Value
public static final java.lang.String	FILTER_NAME	"LowQD"