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);
}
/**
* @param replaceFirst
* @param chromFname
* @param chrom
*/
public static void process(String inVarsName, String outChromName, int chrom) {
ArrayList<Varlet> vars = Varlet.fromTextFile(inVarsName);
ChromosomeArray cha = Data.getChromosome(chrom);
ChromosomeArray chb = new ChromosomeArray(chrom, Gene.PLUS);
// Next location to read in a
int aloc = 0;
// Next location to set in b
int bloc = 0;
for (int i = 0; i < vars.size(); i++) {
Varlet v = vars.get(i);
assert (v.beginLoc >= aloc)
: i + "\n" + vars.get(i - 1) + "\n" + v + "\n"; // Overlapping variations
while (v.beginLoc < aloc) { // skip it, for now.
System.err.print("e");
i++;
if (i >= vars.size()) {
break;
}
v = vars.get(i);
}
if (STAY_NEAR_REF && Tools.absdif(aloc, bloc) >= REF_LIMIT) {
int dif = v.lengthDif();
if (aloc < bloc) { // skip insertions
while (dif > 0) {
// System.err.print("i");
i++;
if (i >= vars.size()) {
break;
}
v = vars.get(i);
dif = v.lengthDif();
}
} else { // skip deletions
while (dif < 0) {
// System.err.print("d");
i++;
if (i >= vars.size()) {
break;
}
v = vars.get(i);
dif = v.lengthDif();
}
}
}
// Advance to variation's beginning
while (aloc < v.beginLoc) {
byte b = cha.get(aloc);
chb.set(bloc, b);
aloc++;
bloc++;
}
// Apply variation
if (v.varType == Variation.SNP) {
String call = v.call;
String ref = v.ref;
if (ref != null && ref.equals("=")) {
ref = null;
}
for (int j = 0; j < call.length(); j++) {
char c = call.charAt(j);
if (ref != null) {
assert (ref.charAt(j) == cha.get(aloc)) : "\n" + i + ", " + v;
}
chb.set(bloc, c);
aloc++;
bloc++;
}
} else if (v.varType == Variation.DELINS) {
String call = v.call;
for (int j = 0; j < call.length(); j++) {
char c = call.charAt(j);
chb.set(bloc, c);
bloc++;
}
aloc += v.lengthRef();
} else if (v.varType == Variation.NOCALL) {
// Do nothing. But, it should have been removed already.
if (!foundNocall) {
System.err.println("*** Warning - found a nocall in input variations ***");
foundNocall = true;
}
} else if (v.varType == Variation.NOREF) {
String call = v.call;
for (int j = 0; j < call.length(); j++) {
char c = call.charAt(j);
assert (cha.get(aloc) == 'N') : cha.get(aloc);
chb.set(bloc, c);
aloc++;
bloc++;
}
} else if (v.varType == Variation.INS) {
String call = v.call;
for (int j = 0; j < call.length(); j++) {
char c = call.charAt(j);
chb.set(bloc, c);
bloc++;
}
} else if (v.varType == Variation.DEL) {
int len = v.lengthRef();
assert (len > 0);
aloc += len;
}
}
// Finish writing array
while (aloc < cha.array.length || aloc <= cha.maxIndex) {
byte c = cha.get(aloc);
chb.set(bloc, c);
aloc++;
bloc++;
}
System.out.println("Length Shift for chr" + chrom + ": \t" + (bloc - aloc));
Data.unload(chrom, true);
cha = null;
if (REGEN_N_BLOCKS) {
chb = regenNBlocks(chb, N_BLOCK_SIZE, N_BLOCK_TRIGGER, N_BLOCK_END_SIZE);
}
chb.resize(chb.maxIndex + 1);
// Can't do this because it is read later
// if(THREADS==1){ReadWrite.writeObjectInThread(cac, outChromName);}
// else{ReadWrite.write(cac, outChromName);}
ReadWrite.write(chb, outChromName, false);
}
