From aa4f60d98035f53ae9490c1fd76519f5388b0fcc Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Jul 2009 17:44:06 +0000
Subject: [PATCH] Make sure that only reads marked as 'mapped' are filtered
 based on validity of alignment.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1217 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/sam/SAMReadValidator.java              | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java b/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
index ba819aa36..a647aa64a 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/SAMReadValidator.java
@@ -66,23 +66,23 @@ public class SAMReadValidator {
      * @param read The read to validate.
      */
     private static void checkInvalidAlignmentEnd( SAMRecord read ) {
-        if( read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() )
+        if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() )
             throw new SAMReadValidationException("Alignment ends prior to its beginning");
     }
 
     private static void checkAlignmentDisagreesWithHeader( SAMFileHeader header, SAMRecord read ) {
         SAMSequenceRecord contigHeader = header.getSequence( read.getReferenceIndex() );
-        if( !read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() ) {
+        if( !read.getReadUnmappedFlag() && read.getAlignmentStart() > contigHeader.getSequenceLength() )
             throw new SAMReadValidationException("Read is aligned to a point after the end of the contig");
-        }
-    }    
+    }
 
     /**
      * Check for inconsistencies between the cigar string and the 
      * @param read The read to validate.
      */
     private static void checkCigarDisagreesWithAlignment( SAMRecord read ) {
-        if( read.getAlignmentStart() != -1 &&
+        if( !read.getReadUnmappedFlag() &&
+            read.getAlignmentStart() != -1 &&
             read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START &&
             read.getAlignmentBlocks().size() == 0 )
             throw new SAMReadValidationException("Read has a valid alignment start, but the CIGAR string is empty");