public class CollectRnaSeqMetrics extends SinglePassSamProgram
Modifier and Type | Field and Description |
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java.io.File |
CHART_OUTPUT |
java.util.Set<java.lang.String> |
IGNORE_SEQUENCE |
java.util.Set<MetricAccumulationLevel> |
METRIC_ACCUMULATION_LEVEL |
int |
MINIMUM_LENGTH |
java.io.File |
REF_FLAT |
java.io.File |
RIBOSOMAL_INTERVALS |
double |
RRNA_FRAGMENT_PERCENTAGE |
RnaSeqMetricsCollector.StrandSpecificity |
STRAND_SPECIFICITY |
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectRnaSeqMetrics() |
Modifier and Type | Method and Description |
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protected void |
acceptRead(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence refSeq)
Should be implemented by subclasses to accept SAMRecords one at a time.
|
protected void |
finish()
Should be implemented by subclasses to do one-time finalization work.
|
static void |
main(java.lang.String[] argv)
Required main method implementation.
|
protected void |
setup(htsjdk.samtools.SAMFileHeader header,
java.io.File samFile)
Should be implemented by subclasses to do one-time initialization work.
|
doWork, makeItSo, usesNoRefReads
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat") public java.io.File REF_FLAT
@Option(doc="Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described <a href=\"http://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html\">here</a>:", optional=true) public java.io.File RIBOSOMAL_INTERVALS
@Option(shortName="STRAND", doc="For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.") public RnaSeqMetricsCollector.StrandSpecificity STRAND_SPECIFICITY
@Option(doc="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater.") public int MINIMUM_LENGTH
@Option(doc="The PDF file to write out a plot of normalized position vs. coverage.", shortName="CHART", optional=true) public java.io.File CHART_OUTPUT
@Option(doc="If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted as ") public java.util.Set<java.lang.String> IGNORE_SEQUENCE
@Option(doc="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA.") public double RRNA_FRAGMENT_PERCENTAGE
@Option(shortName="LEVEL", doc="The level(s) at which to accumulate metrics. ") public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
public static void main(java.lang.String[] argv)
protected void setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile)
SinglePassSamProgram
setup
in class SinglePassSamProgram
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence refSeq)
SinglePassSamProgram
acceptRead
in class SinglePassSamProgram
protected void finish()
SinglePassSamProgram
finish
in class SinglePassSamProgram