Package picard.analysis
Class CollectGcBiasMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.CollectGcBiasMetrics
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@DocumentedFeature public class CollectGcBiasMetrics extends SinglePassSamProgram
Tool to collect information about GC bias in the reads in a given BAM file. Computes the number of windows (of size specified by SCAN_WINDOW_SIZE) in the genome at each GC% and counts the number of read starts in each GC bin. What is output and plotted is the "normalized coverage" in each bin - i.e. the number of reads per window normalized to the average number of reads per window across the whole genome.
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Field Summary
Fields Modifier and Type Field Description boolean
ALSO_IGNORE_DUPLICATES
File
CHART_OUTPUT
boolean
IS_BISULFITE_SEQUENCED
Set<MetricAccumulationLevel>
METRIC_ACCUMULATION_LEVEL
double
MINIMUM_GENOME_FRACTION
int
SCAN_WINDOW_SIZE
File
SUMMARY_OUTPUT
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Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, 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_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 CollectGcBiasMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
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(String[] args)
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, makeItSo, setReferenceSequence, usesNoRefReads
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, 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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CHART_OUTPUT
@Argument(shortName="CHART", doc="The PDF file to render the chart to.") public File CHART_OUTPUT
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SUMMARY_OUTPUT
@Argument(shortName="S", doc="The text file to write summary metrics to.") public File SUMMARY_OUTPUT
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SCAN_WINDOW_SIZE
@Argument(shortName="WINDOW_SIZE", doc="The size of the scanning windows on the reference genome that are used to bin reads.") public int SCAN_WINDOW_SIZE
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MINIMUM_GENOME_FRACTION
@Argument(shortName="MGF", doc="For summary metrics, exclude GC windows that include less than this fraction of the genome.") public double MINIMUM_GENOME_FRACTION
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IS_BISULFITE_SEQUENCED
@Argument(shortName="BS", doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.") public boolean IS_BISULFITE_SEQUENCED
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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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ALSO_IGNORE_DUPLICATES
@Argument(shortName="ALSO_IGNORE_DUPLICATES", doc="Use to get additional results without duplicates. This option allows to gain two plots per level at the same time: one is the usual one and the other excludes duplicates.") public boolean ALSO_IGNORE_DUPLICATES
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Method Detail
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main
public static void main(String[] args)
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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 ref)
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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