Package picard.analysis
Class CollectInsertSizeMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.CollectInsertSizeMetrics
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@DocumentedFeature public class CollectInsertSizeMetrics extends SinglePassSamProgram
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
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Field Summary
Fields Modifier and Type Field Description double
DEVIATIONS
File
Histogram_FILE
protected static String
Histogram_R_SCRIPT
Integer
HISTOGRAM_WIDTH
boolean
INCLUDE_DUPLICATES
Set<MetricAccumulationLevel>
METRIC_ACCUMULATION_LEVEL
Integer
MIN_HISTOGRAM_WIDTH
float
MINIMUM_PCT
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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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectInsertSizeMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
acceptRead(htsjdk.samtools.SAMRecord record, 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.protected boolean
usesNoRefReads()
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.-
Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, getOutputArgumentCollection, makeItSo, setReferenceSequence
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Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, 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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Histogram_R_SCRIPT
protected static final String Histogram_R_SCRIPT
- See Also:
- Constant Field Values
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Histogram_FILE
@Argument(shortName="H", doc="File to write insert size Histogram chart to.") public File Histogram_FILE
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DEVIATIONS
@Argument(doc="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and sd grossly misleading regarding the real distribution.") public double DEVIATIONS
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HISTOGRAM_WIDTH
@Argument(shortName="W", doc="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be included.", optional=true) public Integer HISTOGRAM_WIDTH
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MIN_HISTOGRAM_WIDTH
@Argument(shortName="MW", doc="Minimum width of histogram plots. In the case when the histogram would otherwise betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum range.", optional=true) public Integer MIN_HISTOGRAM_WIDTH
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MINIMUM_PCT
@Argument(shortName="M", doc="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1).") public float MINIMUM_PCT
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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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INCLUDE_DUPLICATES
@Argument(doc="If true, also include reads marked as duplicates in the insert size histogram.") public boolean INCLUDE_DUPLICATES
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Method Detail
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customCommandLineValidation
protected String[] customCommandLineValidation()
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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usesNoRefReads
protected boolean usesNoRefReads()
Description copied from class:SinglePassSamProgram
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.- Overrides:
usesNoRefReads
in classSinglePassSamProgram
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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 record, 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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