@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) {
System.err.println(
"Executing "
+ (new Object() {}.getClass().getEnclosingClass().getName())
+ " "
+ Arrays.toString(args)
+ "\n");
Timer t = new Timer();
String inPattern = args[0];
int minChrom = -1;
int maxChrom = -1;
int outgenome = -1;
Data.GENOME_BUILD = -1;
String name = null;
for (int i = 1; i < args.length; i++) {
final String arg = args[i].toLowerCase();
String[] split = arg.split("=");
String a = split[0];
String b = (split.length > 1 ? split[1] : null);
if (a.equals("ingenome")) {
Data.setGenome(Integer.parseInt(b));
if (minChrom == -1) {
minChrom = 1;
}
if (maxChrom == -1) {
maxChrom = Data.numChroms;
}
} else if (a.equals("outgenome")) {
outgenome = Integer.parseInt(b);
} else if (a.equals("minchrom")) {
minChrom = Integer.parseInt(b);
} else if (a.equals("maxchrom")) {
maxChrom = Integer.parseInt(b);
} else if (a.equals("threads") || a.equals("t")) {
THREADS = Integer.parseInt(b);
} else if (a.equals("nblocksize")) {
N_BLOCK_SIZE = Integer.parseInt(b);
} else if (a.equals("nblocktrigger")) {
N_BLOCK_TRIGGER = Integer.parseInt(b);
} else if (a.equals("staynearref")) {
STAY_NEAR_REF = Tools.parseBoolean(b);
} else if (a.equals("append") || a.equals("app")) {
append = ReadStats.append = Tools.parseBoolean(b);
} else if (a.equals("overwrite") || a.equals("ow")) {
overwrite = Tools.parseBoolean(b);
} else if (a.startsWith("regen")) {
REGEN_N_BLOCKS = Tools.parseBoolean(b);
} else if (a.startsWith("name=")) {
REGEN_N_BLOCKS = Tools.parseBoolean(b);
} else {
System.err.println("Unknown argument " + arg);
}
}
assert (Data.GENOME_BUILD > -1);
assert (outgenome > -1);
// assert(Data.GENOME_BUILD!=outgenome);
if (Data.GENOME_BUILD == outgenome) {
System.out.println("Warning! Overwriting input genome " + outgenome);
}
String fname = Data.chromFname(minChrom, outgenome);
File f = new File(fname.substring(0, fname.lastIndexOf('/')));
// assert(false) : f.getAbsolutePath();
if (!f.exists()) {
f.mkdirs();
}
for (int chrom = minChrom; chrom <= maxChrom; chrom++) {
String outName = Data.chromFname(chrom, outgenome);
assert (overwrite || !new File(outName).exists())
: "Destination " + outName + " already exists.";
// assert(false) : inPattern+", "+outName;
process(inPattern.replaceFirst("#", "" + chrom), outName, chrom);
}
FastaToChromArrays2.writeInfo(
outgenome,
maxChrom,
(name == null ? Data.name : name),
"" + Data.GENOME_BUILD + "_plus_variations",
false,
false);
t.stop();
{
String path = IndexMaker4.fname(1, 1, 12, 1);
int lastSlash = path.lastIndexOf('/');
path = path.substring(0, lastSlash);
File dir = new File(path);
if (dir.exists()) {
System.out.println("Deleting old index for " + outgenome);
for (File f2 : dir.listFiles()) {
if (f2.isFile() && (f2.getName().contains(".int2d") || f2.getName().endsWith(".txt"))) {
f2.delete();
}
}
}
}
// System.out.println("Vars in: \t"+VARS_IN);
// System.out.println("Vars out:\t"+VARS_OUT);
System.out.println();
System.out.println("Time: \t" + t);
}