picard.sam

Class ReorderSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.ReorderSam

public class ReorderSam
extends CommandLineProgram

Reorders a SAM/BAM input file according to the order of contigs in a second reference sequence

Author:

mdepristo

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALLOW_CONTIG_LENGTH_DISCORDANCE
boolean	ALLOW_INCOMPLETE_DICT_CONCORDANCE
java.io.File	INPUT
java.io.File	OUTPUT
java.io.File	REFERENCE

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
ReorderSam()

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[] argv) Required main method implementation.

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 file (bam or sam) to extract reads from.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Output file (bam or sam) to write extracted reads to.")
public java.io.File OUTPUT

REFERENCE

@Option(shortName="R",
        doc="Reference sequence to reorder reads to match.  A sequence dictionary corresponding to the reference fasta is required.  Create one with CreateSequenceDictionary.jar.")
public java.io.File REFERENCE

ALLOW_INCOMPLETE_DICT_CONCORDANCE

@Option(shortName="S",
        doc="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs.  By default, this tool requires a corresponding contig in the new reference for each read contig")
public boolean ALLOW_INCOMPLETE_DICT_CONCORDANCE

ALLOW_CONTIG_LENGTH_DISCORDANCE

@Option(shortName="U",
        doc="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length.  Highly dangerous, only use if you know what you are doing.")
public boolean ALLOW_CONTIG_LENGTH_DISCORDANCE

Constructor Detail

ReorderSam

public ReorderSam()

Method Detail

main

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

Required main method implementation.

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.