picard.analysis

Class CollectRnaSeqMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.CollectRnaSeqMetrics

@DocumentedFeature
public class CollectRnaSeqMetrics
extends SinglePassSamProgram

Field Summary

Fields

Modifier and Type	Field and Description
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

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectRnaSeqMetrics()

Method Summary

Modifier and Type	Method and 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 java.lang.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.
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.

Methods inherited from class picard.analysis.SinglePassSamProgram

doWork, makeItSo, setReferenceSequence, usesNoRefReads

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

REF_FLAT

@Argument(doc="Gene annotations in refFlat form.  Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat")
public java.io.File REF_FLAT

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 java.io.File RIBOSOMAL_INTERVALS

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

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

CHART_OUTPUT

@Argument(doc="The PDF file to write out a plot of normalized position vs. coverage.",
          shortName="CHART",
          optional=true)
public java.io.File CHART_OUTPUT

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 as ")
public java.util.Set<java.lang.String> IGNORE_SEQUENCE

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

METRIC_ACCUMULATION_LEVEL

@Argument(shortName="LEVEL",
          doc="The level(s) at which to accumulate metrics.  ")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

Constructor Detail

CollectRnaSeqMetrics

public CollectRnaSeqMetrics()

Method Detail

main

public static void main(java.lang.String[] argv)

Required main method implementation.

customCommandLineValidation

protected java.lang.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 class CommandLineProgram

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.

setup

protected void setup(htsjdk.samtools.SAMFileHeader header,
                     java.io.File samFile)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time initialization work.

Specified by:

setup in class SinglePassSamProgram

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 class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram