From 880c607d799e728f9cefa0d779393fbc978935fd Mon Sep 17 00:00:00 2001 From: hanna Date: Wed, 2 Mar 2011 01:51:26 +0000 Subject: [PATCH] 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 --- .../sting/gatk/datasources/reads/LowMemoryIntervalSharder.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java index de02c9311..2ce832da8 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java @@ -204,10 +204,7 @@ public class LowMemoryIntervalSharder implements Iterator { 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);