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Disable validation of linear index against original linear index process. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5352 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-03-02 01:51:26 +00:00
parent dc62685a2f
commit 880c607d79
1 changed files with 0 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
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@ -204,10 +204,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
for(GATKChunk chunk: bin.getChunkList()) for(GATKChunk chunk: bin.getChunkList())
chunks.add(chunk.clone()); chunks.add(chunk.clone());
} }
final long referenceLinearIndexMinimumOffset = index.getLinearIndex(initialRegion.getContigIndex()).getMinimumOffset(initialRegion.getStart());
final long linearIndexMinimumOffset = binTree.getLinearIndexEntry(); final long linearIndexMinimumOffset = binTree.getLinearIndexEntry();
if(linearIndexMinimumOffset != referenceLinearIndexMinimumOffset)
throw new ReviewedStingException(String.format("Loaded linear index offset is incorrect; is %d, should be %d",linearIndexMinimumOffset,referenceLinearIndexMinimumOffset));
// Optimize the chunk list with a linear index optimization // Optimize the chunk list with a linear index optimization
chunks = index.optimizeChunkList(chunks,linearIndexMinimumOffset); chunks = index.optimizeChunkList(chunks,linearIndexMinimumOffset);