zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
hanna 2011-03-02 01:51:26 +00:00
parent dc62685a2f
commit 880c607d79
1 changed files with 0 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
View File

@ -204,10 +204,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
for(GATKChunk chunk: bin.getChunkList())
chunks.add(chunk.clone());
}
final long referenceLinearIndexMinimumOffset = index.getLinearIndex(initialRegion.getContigIndex()).getMinimumOffset(initialRegion.getStart());
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
chunks = index.optimizeChunkList(chunks,linearIndexMinimumOffset);