picard.analysis

Class CollectQualityYieldMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectQualityYieldMetrics

public class CollectQualityYieldMetrics
extends CommandLineProgram

Command line program to calibrate quality yield metrics

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectQualityYieldMetrics.QualityYieldMetrics A set of metrics used to describe the general quality of a BAM file

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
java.io.File	OUTPUT
boolean	USE_ORIGINAL_QUALITIES

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
CollectQualityYieldMetrics()

Method Summary

Methods

Modifier and Type	Method and Description
protected int	doWork() Main method for the program.
static void	main(java.lang.String[] argv) Stock main method for a command line program.

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="A SAM or BAM file to process.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The metrics file to write with quality yield metrics.")
public java.io.File OUTPUT

USE_ORIGINAL_QUALITIES

@Option(shortName="OQ",
        doc="If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field.")
public boolean USE_ORIGINAL_QUALITIES

Constructor Detail

CollectQualityYieldMetrics

public CollectQualityYieldMetrics()

Method Detail

main

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

Stock main method for a command line program.

doWork

protected int doWork()

Main method for the program. Checks that all input files are present and readable and that the output file can be written to. Then iterates through all the records accumulating metrics. Finally writes metrics file

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.