zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

HaplotypeCaller now creates MNP and complex substitutions by using LD information to decide if events segregate together on haplotypes. Added unit test.

This commit is contained in:
Ryan Poplin 2012-07-02 16:37:39 -04:00
parent b6093ff02c
commit b807ff63ef
1 changed files with 9 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
View File

@ -25,6 +25,9 @@ public class ClippingRankSumTest extends RankSumTest {
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ClippingRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); }
protected void fillQualsFromPileup(byte ref, List<Byte> alts, ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
return;
// This working implementation below needs to be tested for the UG pipeline
/*
for ( final PileupElement p : pileup ) {
if ( isUsableBase(p) ) {
if ( p.getBase() == ref ) {
@ -34,6 +37,7 @@ public class ClippingRankSumTest extends RankSumTest {
}
}
}
*/
}
protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
@ -53,6 +57,10 @@ public class ClippingRankSumTest extends RankSumTest {
}
protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {
return;
// This working implementation below needs to be tested for the UG pipeline
/*
// equivalent is whether indel likelihoods for reads corresponding to ref allele are more likely than reads corresponding to alt allele ?
HashMap<PileupElement,LinkedHashMap<Allele,Double>> indelLikelihoodMap = IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap();
for (final PileupElement p: pileup) {
@ -78,5 +86,6 @@ public class ClippingRankSumTest extends RankSumTest {
altQuals.add((double)AlignmentUtils.getNumHardClippedBases(p.getRead()));
}
}
*/
}
}