From b95165e39c2d6e09516a97ae16e9902b6134e10e Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 1 Nov 2009 00:33:18 +0000
Subject: [PATCH] Make alignment (temporarily) part of main
 GenomeAnalysisTK.jar.  Add some extra logging errors on failure.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                     |  5 ++++-
 .../bwa/AlignmentValidationWalker.java        | 20 +++++++++++++++++--
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 54d6b678e..d8d384d72 100644
--- a/build.xml
+++ b/build.xml
@@ -104,7 +104,10 @@
         </jar>
 
         <jar jarfile="${dist}/GenomeAnalysisTK.jar">
-            <fileset dir="build" includes="**/gatk/**/*.class"/>
+            <fileset dir="build">
+              <include name="**/gatk/**/*.class"/>
+              <include name="**/alignment/**/*.class"/>
+            </fileset>
             <manifest>
                 <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/>
             </manifest>
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
index 018149c5f..a2f8731fc 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
@@ -61,13 +61,29 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
                 matches &= (alignment.getAlignmentStart() == read.getAlignmentStart());
                 matches &= (alignment.isNegativeStrand() == read.getReadNegativeStrandFlag());
                 matches &= (alignment.getCigar().equals(read.getCigar()));
-                matches &= (alignment.getMappingQuality() == read.getMappingQuality());
+                //matches &= (alignment.getMappingQuality() == read.getMappingQuality());
                 if(matches) break;
             }
         }
 
-        if(!matches)
+        if(!matches) {
+            logger.error("Found mismatch!");
+            logger.error(String.format("Read %s:",read.getReadName()));
+            logger.error(String.format("    Contig index: %d",read.getReferenceIndex()));
+            logger.error(String.format("    Alignment start: %d", read.getAlignmentStart()));
+            logger.error(String.format("    Negative strand: %b", read.getReadNegativeStrandFlag()));
+            logger.error(String.format("    Cigar: %s%n", read.getCigarString()));
+            logger.error(String.format("    Mapping quality: %s%n", read.getMappingQuality()));
+            for(int i = 0; i < alignments.length; i++) {
+                logger.error(String.format("Alignment %d:",i));
+                logger.error(String.format("    Contig index: %d",alignments[i].getContigIndex()));
+                logger.error(String.format("    Alignment start: %d", alignments[i].getAlignmentStart()));
+                logger.error(String.format("    Negative strand: %b", alignments[i].isNegativeStrand()));
+                logger.error(String.format("    Cigar: %s", alignments[i].getCigarString()));
+                logger.error(String.format("    Mapping quality: %s%n", alignments[i].getMappingQuality()));
+            }
             throw new StingException(String.format("Read %s mismatches!", read.getReadName()));
+        }
 
         return 1;
     }