public Bed2Bar(String[] args) { try { processArgs(args); // load Window[] for (int i = 0; i < bedFiles.length; i++) { bedFile = bedFiles[i]; System.out.println("Parsing " + bedFile.getName()); bedLinesHash = Bed.parseBedFile(bedFile, true, false); if (bedLinesHash == null || bedLinesHash.size() == 0) { System.out.println("Problem parsing bed file, skipping!"); continue; } barDirectory = IO.makeDirectory(bedFile, ""); File bedOutFile = new File(Misc.removeExtension(bedFile.toString()) + "_" + threshold + "_Filt.bed"); bedOut = new PrintWriter(new FileWriter(bedOutFile)); makeStairStepBarFiles(); } bedOut.close(); System.out.println("\nDone!\n"); } catch (IOException e) { e.printStackTrace(); } }