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 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()