From d4feb99d9a7a394c9849cbf37dcf72ba1129b8cf Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 22 Oct 2010 05:08:15 +0000 Subject: [PATCH] For parallel ROD traversals, simplified reference sharding. Will replace with a more sensible strategy for sharding w/o BAMs at some point after ASHG. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/datasources/shards/LocusShardStrategy.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java index f80384139..f5003ddb9 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java @@ -94,8 +94,13 @@ public class LocusShardStrategy implements ShardStrategy { } } else { - for(GenomeLoc interval: locations) + for(GenomeLoc interval: locations) { + while(interval.size() > maxShardSize) { + filePointers.add(new FilePointer(GenomeLocParser.createGenomeLoc(interval.getContig(),interval.getStart(),interval.getStart()+maxShardSize-1))); + interval = GenomeLocParser.createGenomeLoc(interval.getContig(),interval.getStart()+maxShardSize,interval.getStop()); + } filePointers.add(new FilePointer(interval)); + } } filePointerIterator = filePointers.iterator(); }