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, 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, SYNTAX_TRANSITION_URL, 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 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 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
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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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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 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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