public static void main(String[] args) {
Timer t = new Timer();
String in = args[0];
String outF = args.length > 1 ? args[1] : null;
String outR = args.length > 2 ? args[2] : null;
String outU = args.length > 3 ? args[3] : null;
if (args.length > 4) {
if (args[4].equalsIgnoreCase("header")) {
includeHeader = true;
}
}
ByteFile tf = ByteFile.makeByteFile(in, true, false);
Tools.testForDuplicateFiles(true, in, outF, outR, outU);
Tools.testOutputFiles(true, false, false, outF, outR, outU);
final ByteStreamWriter fStream, rStream, uStream;
fStream = (outF == null ? null : new ByteStreamWriter(outF, true, false, true));
rStream = (outR == null ? null : new ByteStreamWriter(outR, true, false, true));
uStream = (outU == null ? null : new ByteStreamWriter(outU, true, false, true));
if (fStream != null) {
fStream.start();
}
if (rStream != null) {
rStream.start();
}
if (uStream != null) {
uStream.start();
}
long plus = 0;
long minus = 0;
long other = 0;
byte[] s = null;
for (s = tf.nextLine(); s != null; s = tf.nextLine()) {
if (s.length > 0) {
byte c = s[0];
if (c == '@') {
if (includeHeader) {
if (fStream != null) {
fStream.println(s);
}
if (rStream != null) {
rStream.println(s);
}
if (uStream != null) {
uStream.println(s);
}
}
} else {
int flag = SamLine.parseFlagOnly(s);
if (SamLine.mapped(flag)) {
if (SamLine.strand(flag) == 0) {
if (fStream != null) {
fStream.println(s);
}
plus++;
} else {
if (rStream != null) {
rStream.println(s);
}
minus++;
}
} else {
if (uStream != null) {
uStream.println(s);
}
other++;
}
}
}
}
tf.close();
if (fStream != null) {
fStream.poisonAndWait();
}
if (rStream != null) {
rStream.poisonAndWait();
}
if (uStream != null) {
uStream.poisonAndWait();
}
System.err.println("Total reads: \t" + (plus + minus + other));
System.err.println("Plus reads: \t" + (plus));
System.err.println("Minus reads: \t" + (minus));
System.err.println("Unmapped reads:\t" + (other));
t.stop();
System.err.println("Time: \t" + t);
}
