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Merge pull request #943 from broadinstitute/ldg_fixAllowNonUniqueKmers 

Fix implementation of allowNonUniqueKmersInRef so that it applies to all...
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Geraldine Van der Auwera 2015-04-27 04:08:50 +02:00
parent d4753f189f 97caf94807
commit cb4c3ea09e
1 changed files with 1 additions and 1 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
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@ -124,7 +124,7 @@ public class ReadThreadingAssembler extends LocalAssemblyEngine {
while ( results.isEmpty() && numIterations <= MAX_KMER_ITERATIONS_TO_ATTEMPT ) {
// on the last attempt we will allow low complexity graphs
final boolean lastAttempt = numIterations == MAX_KMER_ITERATIONS_TO_ATTEMPT;
addResult(results, createGraph(reads, refHaplotype, kmerSize, givenHaplotypes, lastAttempt, lastAttempt));
addResult(results, createGraph(reads, refHaplotype, kmerSize, givenHaplotypes, lastAttempt, allowNonUniqueKmersInRef || lastAttempt));
kmerSize += KMER_SIZE_ITERATION_INCREASE;
numIterations++;
}