From c6f6948f9de96a21cadd611ba1b6965f16b9dec7 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 12 Feb 2010 04:51:56 +0000 Subject: [PATCH] Haiku: Eric is a fool. Matt found his really dumb bug. Eric is humbled. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2830 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index c0576cbe0..85e916aea 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -291,14 +291,11 @@ public class IndelRealigner extends ReadWalker { } if ( writers != null ) { - for ( SAMFileWriter writer : writers.values() ) { - // TODO -- figure out why we're getting an exception thrown here - // TODO -- because we need to call close() to flush out the remaining reads from the writer - try { - writer.close(); - if ( !SORT_ON_DISK ) - ((SortingSAMFileWriter)writer).getBaseWriter().close(); - } catch (RuntimeException e) {} + HashSet uniqueWriters = new HashSet(writers.values()); + for ( SAMFileWriter writer : uniqueWriters ) { + writer.close(); + if ( !SORT_ON_DISK ) + ((SortingSAMFileWriter)writer).getBaseWriter().close(); } }