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.

Author:

Tim Fennell

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectMultipleMetrics.Program
static interface	CollectMultipleMetrics.ProgramInterface

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ASSUME_SORTED
java.io.File	DB_SNP
java.lang.String	FILE_EXTENSION
java.io.File	INPUT
java.io.File	INTERVALS
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
java.lang.String	OUTPUT
java.util.Set<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

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.Collection<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

METRIC_ACCUMULATION_LEVEL

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

FILE_EXTENSION

@Option(shortName="EXT",
        doc="Append the given file extension to all metric file names (ex. OUTPUT.insert_size_metrics.EXT). None if null",
        optional=true)
public java.lang.String FILE_EXTENSION

PROGRAM

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

INTERVALS

@Option(doc="An optional list of intervals to restrict analysis to. Only pertains to some of the PROGRAMs. Programs whose stand-alone CLP does not have an INTERVALS argument will silently ignore this argument.",
        optional=true)
public java.io.File INTERVALS

DB_SNP

@Option(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis by some PROGRAMs, PROGRAMS whose CLP doesn\'t allow for this argument will quetly ignore it.",
        optional=true)
public java.io.File DB_SNP

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.Collection<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.