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Merge pull request #788 from broadinstitute/ldg_fixCombineGVCFsBug 

Fixed huge bug from 9895005a (CombineGVCFs used to stop after the first ...
This commit is contained in:
Valentin Ruano Rubio 2014-12-16 15:17:33 -05:00
parent bcc6b73e9b 011843c569
commit 3deaa4832c
1 changed files with 18 additions and 17 deletions
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35
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
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@ -181,11 +181,9 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
if ( startingStates == null )
return previousState;
final int currentPos = startingStates.loc.getStart();
if ( !startingStates.VCs.isEmpty() ) {
if ( ! okayToSkipThisSite(startingStates, previousState) )
endPreviousStates(previousState, currentPos - 1, startingStates, false);
endPreviousStates(previousState, startingStates.loc.incPos(-1), startingStates, false);
previousState.VCs.addAll(startingStates.VCs);
for(final VariantContext vc : previousState.VCs){
previousState.samples.addAll(vc.getSampleNames());
@ -193,8 +191,8 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
}
if ( USE_BP_RESOLUTION || containsEndingContext(previousState.VCs, currentPos) ) {
endPreviousStates(previousState, currentPos, startingStates, true);
if ( USE_BP_RESOLUTION || containsEndingContext(previousState.VCs, startingStates.loc.getStart()) ) {
endPreviousStates(previousState, startingStates.loc, startingStates, true);
}
return previousState;
@ -249,26 +247,29 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
/**
* Disrupt the VariantContexts so that they all stop at the given pos, write them out, and put the remainder back in the list.
*
* @param state the state with list of VariantContexts
* @param pos the target ending position
* @param state the previous state with list of active VariantContexts
* @param pos the position for the starting VCs
* @param startingStates the state for the starting VCs
* @param atCurrentPosition indicates whether we output a variant at the current position, independent of VCF start/end, i.e. in BP resolution mode
*/
private void endPreviousStates(final OverallState state, final int pos, final PositionalState startingStates, boolean atCurrentPosition) {
private void endPreviousStates(final OverallState state, final GenomeLoc pos, final PositionalState startingStates, boolean atCurrentPosition) {
final byte refBase = startingStates.refBases[0];
//if we're in BP resolution mode or a VC ends at the current position then the reference for the next output VC (refNextBase)
// will be advanced one base
final byte refNextBase = (atCurrentPosition) ? (startingStates.refBases.length > 1 ? startingStates.refBases[1] : (byte)'N' ): refBase;
final List<VariantContext> stoppedVCs = new ArrayList<>(state.VCs.size());
for ( int i = state.VCs.size() - 1; i >= 0; i-- ) {
final VariantContext vc = state.VCs.get(i);
if ( vc.getStart() <= pos ) {
//the VC for the previous state will be stopped if its position is previous to the current position or it we've moved to a new contig
if ( vc.getStart() <= pos.getStart() || !vc.getChr().equals(pos.getContig())) {
stoppedVCs.add(vc);
// if it was ending anyways, then remove it from the future state
if ( vc.getEnd() == pos) {
if ( vc.getEnd() == pos.getStart()) {
state.samples.removeAll(vc.getSampleNames());
state.VCs.remove(i);
continue; //don't try to remove twice
@ -282,18 +283,18 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
}
}
//if we already output this state in BP resolution mode (reflected by state.prevPos) then skip output
GenomeLoc lastWriteLoc = state.prevPos;
final int lastWritePos = lastWriteLoc == null ? -1 : lastWriteLoc.getStart();
if ( !stoppedVCs.isEmpty() && pos > lastWritePos) {
final GenomeLoc gLoc = genomeLocParser.createGenomeLoc(stoppedVCs.get(0).getChr(), pos);
//output the stopped VCs if there is no previous output (state.prevPos == null) or our current position is past
// the last write position (state.prevPos)
//NOTE: BP resolution with have current position == state.prevPos because it gets output via a different control flow
if ( !stoppedVCs.isEmpty() && (state.prevPos == null || pos.isPast(state.prevPos) )) {
final GenomeLoc gLoc = genomeLocParser.createGenomeLoc(stoppedVCs.get(0).getChr(), pos.getStart());
// we need the specialized merge if the site contains anything other than ref blocks
final VariantContext mergedVC;
if ( containsTrueAltAllele(stoppedVCs) )
mergedVC = ReferenceConfidenceVariantContextMerger.merge(stoppedVCs, gLoc, refBase, false);
else
mergedVC = referenceBlockMerge(stoppedVCs, state, pos);
mergedVC = referenceBlockMerge(stoppedVCs, state, pos.getStart());
vcfWriter.add(mergedVC);
state.prevPos = gLoc;