public static void printLines(
ArrayList<String[]> lines, boolean uniqueOnly, boolean filterSubOpt) {
double numHits = 0;
ArrayList<String[]> linesToPrint;
// First count the number of (valid) hits
if (filterSubOpt && lines.size() > 1) {
linesToPrint = new ArrayList<String[]>();
int minMis = Integer.MAX_VALUE;
// Find minimum number of mismatchs
int[] mismatches = new int[lines.size()];
int i = 0;
for (String[] pieces : lines) {
int mis = 0;
if (pieces.length > 7 && pieces[7].length() > 1) mis = pieces[7].split(",").length;
mismatches[i] = mis;
if (mis < minMis) minMis = mis;
i++;
}
// Only add minimum mismatch hits
i = 0;
for (String[] pieces : lines) {
if (mismatches[i] == minMis) linesToPrint.add(pieces);
i++;
}
numHits = linesToPrint.size();
} else {
linesToPrint = lines;
numHits = lines.size();
}
// Now add the hits!
if (!uniqueOnly || linesToPrint.size() == 1) {
double weight = 1.0 / numHits;
for (String[] pieces : linesToPrint) {
if (readLength == -1) readLength = pieces[4].length();
Integer coord =
pieces[1].equals("+")
? Integer.valueOf(pieces[3])
: Integer.valueOf(pieces[3]) + readLength - 1;
coord += 1; // Bowtie default output is 0-based - we want 1-based.
System.out.println(
String.format(
"%s\t%s\t%s\t%d\t%f", pieces[2], coord, pieces[1], pieces[4].length(), weight));
}
}
}
private boolean startLauncher(File dir) {
try {
Runtime rt = Runtime.getRuntime();
ArrayList<String> command = new ArrayList<String>();
command.add("java");
command.add("-jar");
command.add("Launcher.jar");
String[] cmdarray = command.toArray(new String[command.size()]);
Process proc = rt.exec(cmdarray, null, dir);
return true;
} catch (Exception ex) {
System.err.println("Unable to start the Launcher program.\n" + ex.getMessage());
return false;
}
}