Class BamIndexStats

java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.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 Details

    • INPUT

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

  • Constructor Details

    • BamIndexStats

      public BamIndexStats()

  • Method Details

    • 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.