Package picard.sam

Class SamFormatConverter


  • @DocumentedFeature
    public class SamFormatConverter
    extends CommandLineProgram
    Converts a BAM file to human-readable SAM output or vice versa
    • Field Detail

      • INPUT

        @Argument(doc="The SAM/BAM/CRAM file to parse.",
                  shortName="I")
        public File INPUT
      • OUTPUT

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

      • SamFormatConverter

        public SamFormatConverter()
    • Method Detail

      • 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.
      • convert

        public static void convert​(File input,
                                   File output,
                                   File referenceSequence,
                                   Boolean createIndex)
        Convert a file from one of sam/bam/cram format to another based on the extension of output.
        Parameters:
        input - input file in one of sam/bam/cram format
        output - output to write converted file to, the conversion is based on the extension of this filename
        referenceSequence - the reference sequence to use, necessary when reading/writing cram
        createIndex - whether or not an index should be written alongside the output file