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Framework works properly now, but whitening still has a kink which is that the covariance matrix gets re-sorted automatically by the eigendecomposition, so somehow the association between eigenvalue and dimension (e.g. association track) needs to be maintained throughout. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5530 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-03-28 22:22:37 +00:00
parent 4c04c5a47a
commit f3e4c24f63
1 changed files with 4 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RegionalAssociationRecalibrator.java
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@ -136,10 +136,12 @@ public class RegionalAssociationRecalibrator extends RodWalker<RegionalAssociati
Arrays.sort(normRanks);
for ( LocHashingPair lhp : normByLoc ) {
int rank = Arrays.binarySearch(normRanks,lhp.second);
// note - equal values will always be assigned the same rank -- however
// it is proper, no need for random assignment.
double prob = ((double) rank)/((double)normRanks.length);
int qual = AssociationTestRunner.pToQ(prob);
out.printf("%s\t%d\t%d\t%d\t%.2e\t%d",lhp.getFirst().getContig(),lhp.getFirst().getStart(),lhp.getFirst().getStop(),
qual,prob,rank);
out.printf("%s\t%d\t%d\t%d\t%.2e\t%d\t%.2e%n",lhp.getFirst().getContig(),lhp.getFirst().getStart(),lhp.getFirst().getStop(),
qual,prob,rank,lhp.getSecond());
}
}