public void run() {
long starttime = System.currentTimeMillis();
ArrayList<String> resultList = new ArrayList();
for (int i = 0; i < tbt.getTagCount(); i++) {
int[] minPresentFamilies = getMinPresentFamily(i, (float) 0.08);
if (minPresentFamilies == null) continue;
ArrayList segregationList =
this.getSegregationFamilyGroups(i, minPresentFamilies, 10, pThresh);
if (segregationList == null) continue;
int[][] segregationFamilyGroups = (int[][]) segregationList.get(0);
int[] bestChrs = (int[]) segregationList.get(1);
int minGnum = segregationFamilyGroups.length;
if (familyGroupNum < minGnum) minGnum = familyGroupNum;
double[][] theResults = new double[minGnum][];
boolean nullFlag = true;
for (int j = 0;
j < minGnum;
j++) { // it should be bestChrs.length, only caculate 2 loci for now
ScanChromosome scanOnBestChrom =
new ScanChromosome(
tbt,
i,
theAnchorChrInBits[bestChrs[j] - 1],
segregationFamilyGroups[j],
j,
theResults,
0.00001,
1);
scanOnBestChrom.scan();
if (theResults[j] == null) continue;
nullFlag = false;
}
if (nullFlag) continue;
resultList.add(this.getOutputRecord(i, theResults));
}
result = resultList.toArray(new String[resultList.size()]);
double secs = (double) (System.currentTimeMillis() - starttime) * 0.001;
System.out.println(
"Task "
+ taskID
+ " with "
+ tbt.getTagCount()
+ " tags is finished in "
+ secs
+ " seconds");
}
public void run() {
long starttime = System.currentTimeMillis();
ArrayList<String> resultList = new ArrayList();
for (int i = 0; i < tbt.getTagCount(); i++) {
if (tbt.getNumberOfTaxaWithTag(i) < 30) continue;
double[] bestR = {-1, -1, -1, 1, -1};
int blastChr = -1, blastPos = -1, bestAlignment = -1, refDiv = -1;
long[] testTag = tbt.getTag(i);
long[] testTagDist;
double[][] theResults = new double[theAnchorChrInBits.length][];
ScanChromosomeMTR[] scanOnChr = new ScanChromosomeMTR[theAnchorChrInBits.length];
for (int cn = 0; cn < theAnchorChrInBits.length; cn++) {
testTagDist =
getTagsInBits(
tbt, i, tbt2anchRedirect[cn], theAnchorChrInBits[cn].getSequenceCount());
scanOnChr[cn] =
new ScanChromosomeMTR(
theAnchorChrInBits[cn], testTagDist, cn, theResults, 0.000001, 1, blastPos);
scanOnChr[cn].scan();
}
int countRealSig = 0;
double[] pRank = new double[theAnchorChrInBits.length];
for (int cn = 0; cn < theAnchorChrInBits.length; cn++) {
double[] r = theResults[cn];
pRank[cn] = r[3];
if (r[3] < bestR[3]) {
bestR = r.clone();
bestAlignment = cn;
}
if (r[3] < 0.000001) countRealSig++;
}
Arrays.sort(pRank);
double[][] bestResWithNewThreshold = new double[1][];
testTagDist =
getTagsInBits(
tbt,
i,
tbt2anchRedirect[bestAlignment],
theAnchorChrInBits[bestAlignment].getSequenceCount());
ScanChromosomeMTR bestChrNewThres =
new ScanChromosomeMTR(
theAnchorChrInBits[bestAlignment],
testTagDist,
0,
bestResWithNewThreshold,
pRank[1],
1,
blastPos);
bestChrNewThres.scan();
int countOfSitesBetterThanNextBestChr = (int) bestResWithNewThreshold[0][4];
String s =
String.format(
"%s %d %d %d %d %d %d %d %g %d %d %d %g %g %d %d %d %n",
BaseEncoder.getSequenceFromLong(testTag),
i,
blastChr,
blastPos,
refDiv,
(int) bestR[0],
(int) bestR[1],
(int) bestR[2],
bestR[3],
(int) bestR[4],
tbt.getNumberOfTaxaWithTag(i),
countRealSig,
Math.log10(pRank[1] / pRank[0]),
Math.log10(pRank[theAnchorChrInBits.length / 2] / pRank[0]),
countOfSitesBetterThanNextBestChr,
bestChrNewThres.minSigPos,
bestChrNewThres.maxSigPos);
resultList.add(s);
}
result = resultList.toArray(new String[resultList.size()]);
double secs = (double) (System.currentTimeMillis() - starttime) * 0.001;
System.out.println(
"Task "
+ taskID
+ " with "
+ tbt.getTagCount()
+ " tags is finished in "
+ secs
+ " seconds");
}