From 1b572b192a54b8df7f901d355ebd1cb93d31827b Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 2 Mar 2010 02:59:14 +0000 Subject: [PATCH] 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 --- .../sting/gatk/executive/LinearMicroScheduler.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 44db167e7..d9aa0e850 100644 --- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -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);