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Fix bug in the HC not respecting the requested pruning

This commit is contained in:
Mark DePristo 2013-03-25 18:29:16 -04:00
parent 78c672676b
commit a97576384d
1 changed files with 1 additions and 0 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -406,6 +406,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
// setup the assembler
assemblyEngine = new DeBruijnAssembler( DEBUG, debugGraphTransformations, minKmer);
assemblyEngine.setErrorCorrectKmers(errorCorrectKmers);
assemblyEngine.setPruneFactor(MIN_PRUNE_FACTOR);
if ( graphWriter != null ) assemblyEngine.setGraphWriter(graphWriter);
if ( useLowQualityBasesForAssembly ) assemblyEngine.setMinBaseQualityToUseInAssembly((byte)1);