Package picard.sam

Class RevertOriginalBaseQualitiesAndAddMateCigar


  • @DocumentedFeature
    public class RevertOriginalBaseQualitiesAndAddMateCigar
    extends CommandLineProgram
    This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files. If the file does not have OQs and already has mate cigar tags, nothing is done. New BAM/BAI/MD5 files are created.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="The input SAM/BAM/CRAM file to revert the state of.")
        public File INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="The output SAM/BAM/CRAM file to create.")
        public File OUTPUT
      • SORT_ORDER

        @Argument(shortName="SO",
                  doc="The sort order to create the reverted output file with.By default, the sort order will be the same as the input.",
                  optional=true)
        public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
      • RESTORE_ORIGINAL_QUALITIES

        @Argument(shortName="OQ",
                  doc="True to restore original qualities from the OQ field to the QUAL field if available.")
        public boolean RESTORE_ORIGINAL_QUALITIES
      • MAX_RECORDS_TO_EXAMINE

        @Argument(doc="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file.")
        public int MAX_RECORDS_TO_EXAMINE
    • Constructor Detail

      • RevertOriginalBaseQualitiesAndAddMateCigar

        public RevertOriginalBaseQualitiesAndAddMateCigar()
    • Method Detail

      • doWork

        public 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.
      • canSkipSAMFile

        public static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile canSkipSAMFile​(File inputFile,
                                                                                               int maxRecordsToExamine,
                                                                                               boolean revertOriginalBaseQualities,
                                                                                               File referenceFasta)
        Checks if we can skip the SAM/BAM/CRAM file when reverting origin base qualities and adding mate cigars.
        Parameters:
        inputFile - the SAM/BAM/CRAM input file
        maxRecordsToExamine - the maximum number of records to examine before quitting
        revertOriginalBaseQualities - true if we are to revert original base qualities, false otherwise
        Returns:
        whether we can skip or not, and the explanation why.