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another intermediate commit to update changes from stable

This commit is contained in:
Mauricio Carneiro 2012-08-09 13:25:07 -04:00
parent a89ff7b5dd
commit 3494a52ddc
1 changed files with 9 additions and 6 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -484,7 +484,7 @@ public class SlidingWindow {
boolean foundEvent = false; boolean foundEvent = false;
Object[] header = windowHeader.toArray(); Object[] header = windowHeader.toArray();
for (int i = start; i<=stop; i++) { for (int i = start; i<=stop; i++) {
nHaplotypes = Math.max(nHaplotypes, ((HeaderElement) header[i]).getNumberOfHaplotypes(MIN_ALT_BASE_PROPORTION_TO_TRIGGER_VARIANT)); nHaplotypes = ((HeaderElement) header[i]).getNumberOfHaplotypes(MIN_ALT_BASE_PROPORTION_TO_TRIGGER_VARIANT);
if (nHaplotypes > nContigs) { if (nHaplotypes > nContigs) {
canCompress = false; canCompress = false;
break; break;
@ -519,6 +519,8 @@ public class SlidingWindow {
removeFromHeader(windowHeader, read); removeFromHeader(windowHeader, read);
} }
} }
for (GATKSAMRecord read : allReads)
readsInWindow.remove(read);
} }
return allReads; return allReads;
} }
@ -538,10 +540,6 @@ public class SlidingWindow {
result.addAll(addToSyntheticReads(windowHeader, 0, start)); result.addAll(addToSyntheticReads(windowHeader, 0, start));
result.addAll(finalizeAndAdd(ConsensusType.BOTH)); result.addAll(finalizeAndAdd(ConsensusType.BOTH));
for (GATKSAMRecord read : allReads) {
readsInWindow.remove(read); // todo -- not optimal, but needs to be done so the next region doesn't try to remove the same reads from the header counts.
}
return result; // finalized reads will be downsampled if necessary return result; // finalized reads will be downsampled if necessary
} }
@ -659,7 +657,7 @@ public class SlidingWindow {
int currentHaplotype = 0; int currentHaplotype = 0;
int refStart = windowHeader.get(start).getLocation(); int refStart = windowHeader.get(start).getLocation();
int refStop = windowHeader.get(stop).getLocation(); int refStop = windowHeader.get(stop).getLocation();
List<GATKSAMRecord> toRemove = new LinkedList<GATKSAMRecord>();
for (GATKSAMRecord read : readsInWindow) { for (GATKSAMRecord read : readsInWindow) {
int haplotype = -1; int haplotype = -1;
@ -688,6 +686,7 @@ public class SlidingWindow {
} }
LinkedList<HeaderElement> header = read.getReadNegativeStrandFlag() ? headersNegStrand.get(haplotype) : headersPosStrand.get(haplotype); LinkedList<HeaderElement> header = read.getReadNegativeStrandFlag() ? headersNegStrand.get(haplotype) : headersPosStrand.get(haplotype);
addToHeader(header, read); addToHeader(header, read);
toRemove.add(read);
} }
} }
} }
@ -697,6 +696,10 @@ public class SlidingWindow {
hetReads.addAll(addToSyntheticReads(header, 0, header.size())); hetReads.addAll(addToSyntheticReads(header, 0, header.size()));
hetReads.add(finalizeRunningConsensus()); hetReads.add(finalizeRunningConsensus());
} }
for (GATKSAMRecord read : toRemove) {
readsInWindow.remove(read);
}
return hetReads; return hetReads;
} }