picard.analysis

Class CollectMultipleMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectMultipleMetrics

public class CollectMultipleMetrics
extends CommandLineProgram

Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectMultipleMetrics.Program
static interface	CollectMultipleMetrics.ProgramInterface This interface allows developers to create Programs to run in addition to the ones defined in the Program enum.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ASSUME_SORTED
java.io.File	INPUT
java.lang.String	OUTPUT
java.util.List<CollectMultipleMetrics.Program>	PROGRAM
int	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
CollectMultipleMetrics()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)
void	setProgramsToRun(java.util.List<CollectMultipleMetrics.ProgramInterface> programsToRun) Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.

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

INPUT

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

ASSUME_SORTED

@Option(doc="If true (default), then the sort order in the header file will be ignored.",
        shortName="AS")
public boolean ASSUME_SORTED

STOP_AFTER

@Option(doc="Stop after processing N reads, mainly for debugging.")
public int STOP_AFTER

OUTPUT

@Option(shortName="O",
        doc="Base name of output files.")
public java.lang.String OUTPUT

PROGRAM

@Option(doc="List of metrics programs to apply during the pass through the SAM file.")
public java.util.List<CollectMultipleMetrics.Program> PROGRAM

Constructor Detail

CollectMultipleMetrics

public CollectMultipleMetrics()

Method Detail

main

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

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

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.

setProgramsToRun

public void setProgramsToRun(java.util.List<CollectMultipleMetrics.ProgramInterface> programsToRun)

Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum. This must be called before doWork().

doWork

public 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.