From 499b3536a4d7d7d48f23dd825bc3e4d76c4c187f Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Sep 2009 16:45:07 +0000
Subject: [PATCH] Changed to use AlignmentUtils.isReadUnmapped() for better
 consistency with SAM spec; also, it is now explicitly enforced that unmapped
 reads have <NO_...> values set for ref contig and start upon "remapping"

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1519 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/utils/GenomicMap.java        | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
index 058d68730..f8d2a6b51 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
@@ -24,10 +24,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.*;
 
 public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeLoc> > >{
 	
@@ -204,7 +201,15 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 	 * @return same read instance that was passed to this method, remapped
 	 */
 	public SAMRecord remapToMasterReference(SAMRecord r, SAMFileHeader h, boolean discardCrossContig) {
-		if ( r.getReadUnmappedFlag() ) return r; // nothing to do if read is unmapped
+		if ( AlignmentUtils.isReadUnmapped(r) ) {
+            // set to NO_... just in case: in principle, SAM format spec allows unmapped reads (with 'unmapped'
+            // flag raised) to have reference contig and start position set to arbitrary values for sorting
+            // purposes; after remapping, these values would make no sense or even cause a crash when reading
+            // remapped bam
+            r.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
+            r.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
+            return r; // nothing to do if read is unmapped
+        }
 		
 		int customStart = r.getAlignmentStart();