Package picard.sam

Class FixMateInformation

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.FixMateInformation

@DocumentedFeature
public class FixMateInformation
extends CommandLineProgram

Summary

This tool ensures that all mate-pair information is in sync between each read and its mate pair. If no OUTPUT file is supplied then the output is written to a temporary file and then copied over the INPUT file (with the original placed in a .old file.) Reads marked with the secondary alignment flag are written to the output file unchanged. However, supplementary reads are corrected so that they point to the primary, non-supplemental mate record.

Usage example:

 java -jar picard.jar FixMateInformation \
       I=input.bam \
       O=fixed_mate.bam \
       ADD_MATE_CIGAR=true
 

Caveats

The program should run with fairly limited memory unless there are many mate pairs that are missing or far apart from each other in the file, as it keeps track of the unmatched mates

Field Summary

Fields

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

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
FixMateInformation()

Method Summary

Modifier and Type	Method	Description
protected void	closeWriter()
protected void	createSamFileWriter(htsjdk.samtools.SAMFileHeader header)
protected int	doWork()	Do the work after command line has been parsed.
protected void	writeAlignment(htsjdk.samtools.SAMRecord sam)

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

INPUT

@Argument(shortName="I",
          doc="The SAM/BAM/CRAM input files to check and fix. Multiple files will be merged and sorted.")
public List<File> INPUT

OUTPUT

@Argument(shortName="O",
          optional=true,
          doc="The output file to write to. If no output file is supplied, the input file is overwritten (only available with single input file).")
public File OUTPUT

SORT_ORDER

@Argument(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

@Argument(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

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

IGNORE_MISSING_MATES

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

out

protected htsjdk.samtools.SAMFileWriter out

Constructor Details

FixMateInformation

public FixMateInformation()

Method Details

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()