From 75a541b479c01b65f8f4348eace263d12e881554 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 1 Mar 2010 23:31:58 +0000 Subject: [PATCH] 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 --- .../sting/gatk/executive/LinearMicroScheduler.java | 2 +- 1 file changed, 1 insertion(+), 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 fe96a0bd6..44db167e7 100644 --- a/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -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);