public void splitIndex(String name, String seq) {
int start = 0;
boolean go = true;
while (go) {
int end = start + numberOfBases;
if (end >= seq.length()) {
end = seq.length();
go = false;
}
String subSeq = seq.substring(start, end);
File binarySeq = new File(indexDirectory, name + "_" + start + "-" + (end - 1));
if (binarySeq.exists()) {
System.out.println("WARNING, " + binarySeq + " already exists, skipping!");
return;
}
Seq.writeBinarySequence(subSeq, binarySeq);
start = end;
}
}
/** This method will process each argument and assign new varibles */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'f':
fastas = IO.extractFiles(args[i + 1], "fasta");
i++;
break;
case 'n':
numberOfBases = Integer.parseInt(args[i + 1]);
i++;
break;
case 'i':
indexDirectory = new File(args[i + 1]);
i++;
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printExit("\nError: unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// make index directory?
if (indexDirectory == null) {
indexDirectory = new File(fastas[0].getParentFile(), "IndexedSequences");
indexDirectory.mkdir();
}
}