/** * Main method for the program. Checks that input file is present and readable, then iterates * through the index printing meta data to stdout. */ protected int doWork() { if (INPUT.getName().endsWith(BAMIndex.BAMIndexSuffix)) log.warn("INPUT should be the BAM file name, not its index file"); IOUtil.assertFileIsReadable(INPUT); BAMIndexMetaData.printIndexStats(INPUT); return 0; }