From 63b709d992f11c777e03e6134354be1cc60829b9 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 26 Jan 2011 19:49:07 +0000
Subject: [PATCH] When remapping the read, set MAPQ, CIGAR etc to 0/null for
 unmapped reads. This is not required according to spec but current samtools
 jdk otherwise dies in STRICT validation mode.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5089 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/utils/GenomicMap.java            | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
index 49c136874..ee3b03805 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
@@ -232,6 +232,17 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
             // remapped bam
             r.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
             r.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
+
+            // these are required because current santools jdk is over-validating and requiring MAPQ, CIGAR etc be
+            // set to 0/null for unmapped reads. In principle, it should not matter.
+            r.setMappingQuality(0);
+            r.setCigar(new Cigar());
+            r.setNotPrimaryAlignmentFlag(false);
+            if ( r.getReadNegativeStrandFlag() ) {
+                r.setReadBases(BaseUtils.simpleReverseComplement(r.getReadBases()));
+                r.setBaseQualities(Utils.reverse(r.getBaseQualities()));
+                r.setReadNegativeStrandFlag(false);
+            }
             return r; // nothing to do if read is unmapped
         }