picard.analysis

Class CollectInsertSizeMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.CollectInsertSizeMetrics

public class CollectInsertSizeMetrics
extends SinglePassSamProgram

Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.

Author:

Doug Voet (dvoet at broadinstitute dot org)

Field Summary

Fields

Modifier and Type	Field and Description
double	DEVIATIONS
java.io.File	Histogram_FILE
protected static java.lang.String	Histogram_R_SCRIPT
java.lang.Integer	HISTOGRAM_WIDTH
boolean	INCLUDE_DUPLICATES
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
float	MINIMUM_PCT

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectInsertSizeMetrics()

Method Summary

Modifier and Type	Method and 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 java.lang.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.
static void	main(java.lang.String[] argv) Required main method implementation.
protected void	setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile) Should be implemented by subclasses to do one-time initialization work.
protected boolean	usesNoRefReads() Can be overriden 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, makeItSo

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

Histogram_R_SCRIPT

protected static final java.lang.String Histogram_R_SCRIPT

See Also:

Constant Field Values

Histogram_FILE

@Option(shortName="H",
        doc="File to write insert size Histogram chart to.")
public java.io.File Histogram_FILE

DEVIATIONS

@Option(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

HISTOGRAM_WIDTH

@Option(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 java.lang.Integer HISTOGRAM_WIDTH

MINIMUM_PCT

@Option(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

METRIC_ACCUMULATION_LEVEL

@Option(shortName="LEVEL",
        doc="The level(s) at which to accumulate metrics.  ")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

INCLUDE_DUPLICATES

@Option(doc="If true, also include reads marked as duplicates in the insert size histogram.")
public boolean INCLUDE_DUPLICATES

Constructor Detail

CollectInsertSizeMetrics

public CollectInsertSizeMetrics()

Method Detail

main

public static void main(java.lang.String[] argv)

Required main method implementation.

customCommandLineValidation

protected java.lang.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 class CommandLineProgram

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.

usesNoRefReads

protected boolean usesNoRefReads()

Description copied from class: SinglePassSamProgram

Can be overriden and set to false if the section of unmapped reads at the end of the file isn't needed.

Overrides:

usesNoRefReads in class SinglePassSamProgram

setup

protected void setup(htsjdk.samtools.SAMFileHeader header,
                     java.io.File samFile)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time initialization work.

Specified by:

setup in class SinglePassSamProgram

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 class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram