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Trivial change to LeftAlignVariants: make walker return number of aligned variants on map(), and print out the # of aligned variants at the end of the traversal. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4595 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-10-29 02:03:36 +00:00
parent 2f8057bf24
commit 9a60e72364
1 changed files with 24 additions and 13 deletions
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37
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -76,26 +76,35 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
return 0; return 0;
Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false); Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
for ( VariantContext vc : VCs )
alignAndWrite(vc, ref);
return 0; int changedSites = 0;
for ( VariantContext vc : VCs )
changedSites += alignAndWrite(vc, ref);
return changedSites;
} }
public Integer reduceInit() { return 0; } public Integer reduceInit() { return 0; }
public Integer reduce(Integer value, Integer sum) { return 0; } public Integer reduce(Integer value, Integer sum) {
return sum + value;
public void onTraversalDone(Integer result) {}
private void alignAndWrite(VariantContext vc, final ReferenceContext ref) {
if ( vc.isBiallelic() && vc.isIndel() )
writeLeftAlignedIndel(vc, ref);
else
writer.add(vc, ref.getBase());
} }
private void writeLeftAlignedIndel(final VariantContext vc, final ReferenceContext ref) { public void onTraversalDone(Integer result) {
System.out.println(result + " variants were aligned");
}
private int alignAndWrite(VariantContext vc, final ReferenceContext ref) {
if ( vc.isBiallelic() && vc.isIndel() )
return writeLeftAlignedIndel(vc, ref);
else {
writer.add(vc, ref.getBase());
return 0;
}
}
private int writeLeftAlignedIndel(final VariantContext vc, final ReferenceContext ref) {
final byte[] refSeq = ref.getBases(); final byte[] refSeq = ref.getBases();
// get the indel length // get the indel length
@ -133,8 +142,10 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
newVC = updateAllele(newVC, newAllele); newVC = updateAllele(newVC, newAllele);
writer.add(newVC, refSeq[indelIndex-1]); writer.add(newVC, refSeq[indelIndex-1]);
return 1;
} else { } else {
writer.add(vc, ref.getBase()); writer.add(vc, ref.getBase());
return 0;
} }
} }