Package picard.analysis
Class CollectRnaSeqMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.CollectRnaSeqMetrics
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@DocumentedFeature public class CollectRnaSeqMetrics extends SinglePassSamProgram
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Field Summary
Fields Modifier and Type Field Description File
CHART_OUTPUT
Set<String>
IGNORE_SEQUENCE
Set<MetricAccumulationLevel>
METRIC_ACCUMULATION_LEVEL
int
MINIMUM_LENGTH
File
REF_FLAT
File
RIBOSOMAL_INTERVALS
double
RRNA_FRAGMENT_PERCENTAGE
RnaSeqMetricsCollector.StrandSpecificity
STRAND_SPECIFICITY
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Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTER
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectRnaSeqMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected void
finish()
Should be implemented by subclasses to do one-time finalization work.protected void
setup(htsjdk.samtools.SAMFileHeader header, File samFile)
Should be implemented by subclasses to do one-time initialization work.-
Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, getOutputArgumentCollection, makeItSo, setReferenceSequence, usesNoRefReads
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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REF_FLAT
@Argument(doc="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat") public File REF_FLAT
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RIBOSOMAL_INTERVALS
@Argument(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 File RIBOSOMAL_INTERVALS
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STRAND_SPECIFICITY
@Argument(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
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MINIMUM_LENGTH
@Argument(doc="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater.") public int MINIMUM_LENGTH
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CHART_OUTPUT
@Argument(doc="The PDF file to write out a plot of normalized position vs. coverage.", shortName="CHART", optional=true) public File CHART_OUTPUT
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IGNORE_SEQUENCE
@Argument(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 towards any metrics, except for the PF_BASES field.", optional=true) public Set<String> IGNORE_SEQUENCE
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RRNA_FRAGMENT_PERCENTAGE
@Argument(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
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METRIC_ACCUMULATION_LEVEL
@Argument(shortName="LEVEL", doc="The level(s) at which to accumulate metrics. ") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
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Method Detail
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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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setup
protected void setup(htsjdk.samtools.SAMFileHeader header, File samFile)
Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.- Specified by:
setup
in classSinglePassSamProgram
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acceptRead
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence refSeq)
Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.- Specified by:
acceptRead
in classSinglePassSamProgram
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finish
protected void finish()
Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.- Specified by:
finish
in classSinglePassSamProgram
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