Package picard.analysis
Class MeanQualityByCycle
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.MeanQualityByCycle
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@DocumentedFeature public class MeanQualityByCycle extends SinglePassSamProgram
Program to generate a data table and chart of mean quality by cycle from a BAM file. Works best on a single lane/run of data, but can be applied to merged BAMs - the output may just be a little confusing.
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Field Summary
Fields Modifier and Type Field Description boolean
ALIGNED_READS_ONLY
File
CHART_OUTPUT
boolean
PF_READS_ONLY
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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 MeanQualityByCycle()
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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)
Required main method.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="A file (with .pdf extension) to write the chart to.") public File CHART_OUTPUT
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ALIGNED_READS_ONLY
@Argument(doc="If set to true, calculate mean quality over aligned reads only.") public boolean ALIGNED_READS_ONLY
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PF_READS_ONLY
@Argument(doc="If set to true calculate mean quality over PF reads only.") public boolean PF_READS_ONLY
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Method Detail
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main
public static void main(String[] args)
Required main method.
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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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