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();
}
}
