From 49550e257fff0fbf4ab92a08b86e1fb05e6b9add Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 19 Apr 2011 00:52:13 +0000 Subject: [PATCH] Fix for JamesP's issue. This issue appeared because of a design flaw in the interface between SAMDataSource and IntervalSharder that needs to stay around until the original BAM sharder is retired. Will add a JIRA to fix design flaw. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5661 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/datasources/reads/FilePointer.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java index 469364df8..e322e0cff 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java @@ -108,7 +108,8 @@ class FilePointer { while(thisIterator.hasNext()) { // If there are no elements left in the 'other' iterator, spin out this iterator. if(!otherIterator.hasNext()) { - difference += ((GATKBAMFileSpan)thisIterator.next()).size(); + GATKBAMFileSpan nextSpan = (GATKBAMFileSpan)thisIterator.next().getValue(); + difference += nextSpan.size(); continue; }