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Fix nasty issue where shard boundaries aren't properly clipped during locus traversals. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2907 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2010-03-01 23:31:58 +00:00
parent 9298e13201
commit 75a541b479
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -50,7 +50,7 @@ public class LinearMicroScheduler extends MicroScheduler {
for (Shard shard : shardStrategy) {
// New experimental code for managing locus intervals.
// TODO: we'll need a similar but slightly different strategy for dealing with read intervals, so generalize this code.
if(shard.getShardType() == Shard.ShardType.LOCUS_INTERVAL) {
if(shard.getShardType() == Shard.ShardType.LOCUS || shard.getShardType() == Shard.ShardType.LOCUS_INTERVAL) {
WindowMaker windowMaker = new WindowMaker(getReadIterator(shard),shard.getGenomeLocs());
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
ShardDataProvider dataProvider = new ShardDataProvider(shard,iterator.getLocus(),iterator,reference,rods);