picard.analysis

Class CollectWgsMetricsFromQuerySorted

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetricsFromQuerySorted

public class CollectWgsMetricsFromQuerySorted
extends CommandLineProgram

Computes a number of metrics that are useful for evaluating coverage and performance of sequencing experiments.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics Metrics for evaluating the performance of whole genome sequencing experiments.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
int	MINIMUM_BASE_QUALITY
int	MINIMUM_MAPPING_QUALITY
java.io.File	OUTPUT

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
CollectWgsMetricsFromQuerySorted()

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="Input SAM or BAM file.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Output metrics file.")
public java.io.File OUTPUT

MINIMUM_MAPPING_QUALITY

@Option(shortName="MQ",
        doc="Minimum mapping quality for a read to contribute coverage.",
        overridable=true)
public int MINIMUM_MAPPING_QUALITY

MINIMUM_BASE_QUALITY

@Option(shortName="Q",
        doc="Minimum base quality for a base to contribute coverage.",
        overridable=true)
public int MINIMUM_BASE_QUALITY

Constructor Detail

CollectWgsMetricsFromQuerySorted

public CollectWgsMetricsFromQuerySorted()

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.