picard.sam

Class FilterSamReads

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.FilterSamReads

public class FilterSamReads
extends CommandLineProgram

From a SAM or BAM file, produce a new SAM or BAM by filtering aligned reads or a list of read names provided in a file (one readname per line)

$Id$

Field Summary

Fields

Modifier and Type	Field and Description
picard.sam.FilterSamReads.Filter	FILTER
java.io.File	INPUT
java.io.File	OUTPUT
java.io.File	READ_LIST_FILE
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER
boolean	WRITE_READS_FILES

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
FilterSamReads()

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.
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args) Stock main method.

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(doc="The SAM or BAM file that will be filtered.",
        optional=false,
        shortName="I")
public java.io.File INPUT

FILTER

@Option(doc="Filter.",
        optional=false)
public picard.sam.FilterSamReads.Filter FILTER

READ_LIST_FILE

@Option(doc="Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file.",
        optional=true,
        shortName="RLF")
public java.io.File READ_LIST_FILE

SORT_ORDER

@Option(doc="SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file.",
        optional=true,
        shortName="SO")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

WRITE_READS_FILES

@Option(doc="Create .reads files (for debugging purposes)",
        optional=true)
public boolean WRITE_READS_FILES

OUTPUT

@Option(doc="SAM or BAM file to write read excluded results to",
        optional=false,
        shortName="O")
public java.io.File OUTPUT

Constructor Detail

FilterSamReads

public FilterSamReads()

Method Detail

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.

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.

main

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

Stock main method.

Parameters:

args - main arguments