private void checkForGzippedVcf() { String vcfName = finalVcf.getName(); if (vcfName.endsWith(".gz")) { File uncomp = new File(finalVcf.getParentFile(), vcfName.substring(0, vcfName.length() - 3)); if (uncomp.exists() == false) { deleteTempVcf = true; if (IO.uncompress(finalVcf, uncomp) == null) Misc.printErrAndExit("ERROR: failed to uncompress -> " + finalVcf); } finalVcf = uncomp; } }