From 429582589f7e8b73527c76be3f6227711249c1f3 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Tue, 26 Nov 2013 15:53:29 -0500 Subject: [PATCH] Set SAMFileWriter to create index in ReadUtils to fix SplitSamFile issue --- .../src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index ab866013f..39f227840 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -152,8 +152,8 @@ public class ReadUtils { public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) { validateCompressionLevel(compression); if (file.endsWith(".bam")) - return new SAMFileWriterFactory().makeBAMWriter(header, presorted, new File(file), compression); - return new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, new File(file)); + return new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, presorted, new File(file), compression); + return new SAMFileWriterFactory().setCreateIndex(true).makeSAMOrBAMWriter(header, presorted, new File(file)); } public static int validateCompressionLevel(final int requestedCompressionLevel) {