picard.sam

Class FixMateInformation

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.FixMateInformation

public class FixMateInformation
extends CommandLineProgram

Class to fix mate pair information for all reads in a SAM file. Will run in fairly limited memory unless there are lots of mate pairs that are far apart from each other in the file.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.Boolean	ADD_MATE_CIGAR
boolean	ASSUME_SORTED
java.lang.Boolean	IGNORE_MISSING_MATES
java.util.List<java.io.File>	INPUT
protected htsjdk.samtools.SAMFileWriter	out
java.io.File	OUTPUT
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER

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
FixMateInformation()

Method Summary

Modifier and Type	Method and Description
protected void	closeWriter()
protected void	createSamFileWriter(htsjdk.samtools.SAMFileHeader header)
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args)
protected void	writeAlignment(htsjdk.samtools.SAMRecord sam)

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="The input file to check and fix.")
public java.util.List<java.io.File> INPUT

OUTPUT

@Option(shortName="O",
        optional=true,
        doc="The output file to write to. If no output file is supplied, the input file is overwritten.")
public java.io.File OUTPUT

SORT_ORDER

@Option(shortName="SO",
        optional=true,
        doc="Optional sort order if the OUTPUT file should be sorted differently than the INPUT file.")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

ASSUME_SORTED

@Option(doc="If true, assume that the input file is queryname sorted, even if the header says otherwise.",
        shortName="AS")
public boolean ASSUME_SORTED

ADD_MATE_CIGAR

@Option(shortName="MC",
        optional=true,
        doc="Adds the mate CIGAR tag (MC) if true, does not if false.")
public java.lang.Boolean ADD_MATE_CIGAR

IGNORE_MISSING_MATES

@Option(doc="If true, ignore missing mates, otherwise will throw an exception when missing mates are found.",
        optional=true)
public java.lang.Boolean IGNORE_MISSING_MATES

out

protected htsjdk.samtools.SAMFileWriter out

Constructor Detail

FixMateInformation

public FixMateInformation()

Method Detail

main

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

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.

createSamFileWriter

protected void createSamFileWriter(htsjdk.samtools.SAMFileHeader header)

writeAlignment

protected void writeAlignment(htsjdk.samtools.SAMRecord sam)

closeWriter

protected void closeWriter()