Package picard.sam

Class BamIndexStats


  • @DocumentedFeature
    public class BamIndexStats
    extends CommandLineProgram
    Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate. Similar to the 'samtools idxstats' command.
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="A BAM file to process.")
        public File INPUT
    • Constructor Detail

      • BamIndexStats

        public BamIndexStats()
    • Method Detail

      • doWork

        protected int doWork()
        Main method for the program. Checks that input file is present and readable, then iterates through the index printing meta data to stdout.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.