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Fix bug in ReadThreadingAssembler in cycle failures causing NPE

This commit is contained in:
Mark DePristo 2013-06-25 10:53:33 -04:00
parent e3e8631ff5
commit ed0b1c5aba
1 changed files with 7 additions and 2 deletions
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9
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
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@ -99,13 +99,18 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
this.justReturnRawGraph = justReturnRawGraph;
}
private void addResult(final List<AssemblyResult> results, final AssemblyResult maybeNullResult) {
if ( maybeNullResult != null )
results.add(maybeNullResult);
}
@Override
public List<AssemblyResult> assemble(final List<GATKSAMRecord> reads, final Haplotype refHaplotype, final List<Haplotype> activeAlleleHaplotypes) {
final List<AssemblyResult> results = new LinkedList<>();
// first, try using the requested kmer sizes
for ( final int kmerSize : kmerSizes ) {
results.add(createGraph(reads, refHaplotype, kmerSize, activeAlleleHaplotypes, dontIncreaseKmerSizesForCycles));
addResult(results, createGraph(reads, refHaplotype, kmerSize, activeAlleleHaplotypes, dontIncreaseKmerSizesForCycles));
}
// if none of those worked, iterate over larger sizes if allowed to do so
@ -114,7 +119,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
int numIterations = 1;
while ( results.isEmpty() && numIterations <= MAX_KMER_ITERATIONS_TO_ATTEMPT ) {
// on the last attempt we will allow low complexity graphs
results.add(createGraph(reads, refHaplotype, kmerSize, activeAlleleHaplotypes, numIterations == MAX_KMER_ITERATIONS_TO_ATTEMPT));
addResult(results, createGraph(reads, refHaplotype, kmerSize, activeAlleleHaplotypes, numIterations == MAX_KMER_ITERATIONS_TO_ATTEMPT));
kmerSize += KMER_SIZE_ITERATION_INCREASE;
numIterations++;
}