public void run() {
System.out.println("Chromosome " + chrom + " start loading at " + getCurrentTime());
a = ImportUtils.readFromHapmap(filename, chrom);
chrInBits = new SBitAlignment(a);
System.out.println(
"Chromosome " + chrInBits.getLocusName(0) + " is loaded " + getCurrentTime());
}
private void loadAnchorMaps(String anchorFileName) {
System.out.println("Alignment Loaded:" + anchorFileName);
if (anchorFileName.contains("+") || anchorFileName.contains("=")) {
theAnchorChrInBits = new SBitAlignment[ancChrCnt];
LoadChr[] lc = new LoadChr[ancChrCnt];
Thread[] lt = new Thread[ancChrCnt];
for (int i = 0; i < ancChrCnt; i++) {
System.out.println("anchorFileName " + anchorFileName);
String file = anchorFileName.replace("+", "" + (i + 1));
file = file.replace("=", "" + (i + 1));
System.out.println("Reading:" + file);
lc[i] = new LoadChr(file, "" + (i + 1));
lt[i] = new Thread(lc[i]);
lt[i].start();
}
for (int i = 0; i < lt.length; i++) {
try {
lt[i].join();
} catch (Exception e) {
System.out.println(e.toString());
System.exit(1);
}
}
for (int i = 0; i < lc.length; i++) {
theAnchorChrInBits[i] = lc[i].getBitAlignment();
System.out.printf(
"Chr %s Sites %d Taxa %d %n",
theAnchorChrInBits[i].getLocus(0),
theAnchorChrInBits[i].getSiteCount(),
theAnchorChrInBits[i].getSequenceCount());
}
System.out.println(
"maxMemory: "
+ Runtime.getRuntime().maxMemory() / 1024 / 1024
+ "Mb; freeMemory: "
+ Runtime.getRuntime().freeMemory() / 1024 / 1024
+ "Mb");
} else {
Alignment[] a = ImportUtils.readFromHapmap(anchorFileName).getAlignments();
theAnchorChrInBits = new SBitAlignment[a.length];
for (int i = 0; i < a.length; i++) {
theAnchorChrInBits[i] = new SBitAlignment(a[i]);
// System.out.printf("Chr %d Sites %d Taxa %d %n",
// theAnchorChrInBits[i].getChr(),
//
// theAnchorChrInBits[i].getNumSites(),theAnchorChrInBits[i].getNumTaxa());
System.out.printf(
"Chr %s Sites %d Taxa %d %n",
theAnchorChrInBits[i].getLocus(0),
theAnchorChrInBits[i].getSiteCount(),
theAnchorChrInBits[i].getSequenceCount());
}
}
System.out.println("Anchor maps load at " + this.getCurrentTime());
}