picard.sam

Class DownsampleSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.DownsampleSam

public class DownsampleSam
extends CommandLineProgram

Class to randomly downsample a BAM file while respecting that we should either retain or discard all of the reads for a template - i.e. all reads with the same name, whether first or second of pair, secondary or supplementary, all travel together.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
double	ACCURACY
java.io.File	INPUT
java.io.File	OUTPUT
double	PROBABILITY
java.lang.Integer	RANDOM_SEED
htsjdk.samtools.DownsamplingIteratorFactory.Strategy	STRATEGY

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
DownsampleSam()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, 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

INPUT

@Option(shortName="I",
        doc="The input SAM or BAM file to downsample.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The output, downsampled, SAM or BAM file to write.")
public java.io.File OUTPUT

STRATEGY

@Option(shortName="S",
        doc="The downsampling strategy to use. See usage for discussion.")
public htsjdk.samtools.DownsamplingIteratorFactory.Strategy STRATEGY

RANDOM_SEED

@Option(shortName="R",
        doc="Random seed to use if deterministic behavior is desired.  Setting to null will cause multiple invocations to produce different results.")
public java.lang.Integer RANDOM_SEED

PROBABILITY

@Option(shortName="P",
        doc="The probability of keeping any individual read, between 0 and 1.")
public double PROBABILITY

ACCURACY

@Option(shortName="A",
        doc="The accuracy that the downsampler should try to achieve if the selected strategy supports it. Note that accuracy is never guaranteed, but some strategies will attempt to provide accuracy within the requested bounds.Higher accuracy will generally require more memory.")
public double ACCURACY

Constructor Detail

DownsampleSam

public DownsampleSam()

Method Detail

main

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

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.