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Stopgap fix for temporary problems sharding when indexless. A more compelling solution will come later this week. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2908 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-02 02:59:14 +00:00
parent 75a541b479
commit 1b572b192a
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -50,7 +50,8 @@ 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 || shard.getShardType() == Shard.ShardType.LOCUS_INTERVAL) {
if((shard.getShardType() == Shard.ShardType.LOCUS || shard.getShardType() == Shard.ShardType.LOCUS_INTERVAL) &&
shard.getGenomeLocs().size() > 0) {
WindowMaker windowMaker = new WindowMaker(getReadIterator(shard),shard.getGenomeLocs());
for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
ShardDataProvider dataProvider = new ShardDataProvider(shard,iterator.getLocus(),iterator,reference,rods);