Package picard.analysis
Class CollectGcBiasMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.CollectGcBiasMetrics
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
FieldsModifier and TypeFieldDescriptionboolean
boolean
double
int
Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTER
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, 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 -
Method Summary
Modifier and TypeMethodDescriptionprotected 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[]
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
Should be implemented by subclasses to do one-time initialization work.Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, getOutputArgumentCollection, makeItSo, setReferenceSequence, usesNoRefReads
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 Details
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CHART_OUTPUT
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SUMMARY_OUTPUT
@Argument(shortName="S", doc="The text file to write summary metrics to.") public File SUMMARY_OUTPUT -
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 -
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 -
IS_BISULFITE_SEQUENCED
@Argument(shortName="BS", doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.") public boolean IS_BISULFITE_SEQUENCED -
METRIC_ACCUMULATION_LEVEL
@Argument(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL -
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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Constructor Details
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CollectGcBiasMetrics
public CollectGcBiasMetrics()
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Method Details
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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
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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