@Override
public boolean parseArgument(String arg, String a, String b) {
// System.err.println("Calling parseArgument("+arg+","+a+","+b+")");
if (a.equals("minq")) {
minq = (int) Tools.parseKMG(b);
return true;
} else if (a.equals("maxq")) {
maxq = (int) Tools.parseKMG(b);
return true;
} else if (a.equals("keepperfect")) {
keepPerfect = Tools.parseBoolean(b);
return true;
} else if (a.equals("countindels")) {
countIndels = Tools.parseBoolean(b);
return true;
}
// There was no match to the argument
return false;
}
public static void main(String[] args) {
String in1 = args[0];
String in2 =
(args.length < 2 || args[1].equalsIgnoreCase("null") || args[1].contains("=")
? null
: args[1]);
if (in2 != null) {
assert (!in1.equalsIgnoreCase(in2));
FASTQ.TEST_INTERLEAVED = false;
} else {
FASTQ.TEST_INTERLEAVED = true;
FASTQ.FORCE_INTERLEAVED = true;
}
long maxReads = -1;
for (int i = 1; i < args.length; i++) {
final String arg = args[i];
final String[] split = arg.split("=");
String a = split[0].toLowerCase();
String b = (split.length > 1 ? split[1] : "true");
if (Parser.isJavaFlag(arg)) {
// jvm argument; do nothing
} else if (Parser.parseZip(arg, a, b)) {
// do nothing
} else if (Parser.parseQuality(arg, a, b)) {
// do nothing
} else if (Parser.parseFasta(arg, a, b)) {
// do nothing
} else if (a.equals("reads") || a.startsWith("maxreads")) {
maxReads = Tools.parseKMG(b);
} else {
throw new RuntimeException("Unknown parameter " + args[i]);
}
}
Parser.processQuality();
assert (FastaReadInputStream.settingsOK());
Timer t = new Timer();
ConcurrentReadInputStream cris = getReadInputStream(maxReads, false, true, in1, in2);
System.out.println("Fetched " + cris.getClass().getName());
{
Object[] p = cris.producers();
// while(p[0]==null){
// p=cris.producers();
// }
System.out.print("Producers: ");
String comma = "";
for (Object o : p) {
System.out.print(comma + (o == null ? "null" : o.getClass().getName()));
comma = ", ";
}
System.out.println();
}
boolean paired = cris.paired();
System.out.println("paired=" + paired);
cris.start(); // 4567
ListNum<Read> ln = cris.nextList();
ArrayList<Read> reads = (ln != null ? ln.list : null);
if (reads != null && !reads.isEmpty()) {
Read r = reads.get(0);
assert ((r.mate != null) == paired);
}
long readCount = 0;
long baseCount = 0;
while (reads != null && reads.size() > 0) {
for (Read r : reads) {
Read r2 = r.mate;
if (r != null) {
readCount++;
if (r.bases != null) {
baseCount += r.length();
}
}
if (r2 != null) {
readCount++;
if (r2.bases != null) {
baseCount += r2.length();
}
}
}
cris.returnList(ln.id, ln.list.isEmpty());
// System.err.println("fetching list");
ln = cris.nextList();
reads = (ln != null ? ln.list : null);
// System.out.println("reads: "+(reads==null ? "null" : reads.size()));
}
System.err.println("Finished reading");
cris.returnList(ln.id, ln.list.isEmpty());
cris.close();
t.stop();
System.out.println("Reads: \t" + readCount);
System.out.println("Bases: \t" + baseCount);
System.out.println("Avg Length: \t" + String.format("%.2f", baseCount * 1.0 / readCount));
System.out.println("Time: \t" + t);
}