From dd6122f68200768518384aa93f2deee8fadccaf2 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 7 Mar 2010 15:32:18 +0000
Subject: [PATCH] Fixed another bug in the original sharding system.  Updated
 integration tests as appropriate.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/IndexDrivenSAMDataSource.java    | 10 +++++++---
 .../datasources/simpleDataSources/SAMDataSource.java   |  3 +++
 .../RecalibrationWalkersIntegrationTest.java           |  6 +++---
 3 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/IndexDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/IndexDrivenSAMDataSource.java
index bfa952cd7..ecea7939e 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/IndexDrivenSAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/IndexDrivenSAMDataSource.java
@@ -169,9 +169,13 @@ public class IndexDrivenSAMDataSource extends SAMDataSource {
             if(shard.getGenomeLocs().size() > 1)
                 throw new StingException("This SAMDataSource does not support multiple intervals within a single shard");
             GenomeLoc shardGenomeLoc = shard.getGenomeLocs().get(0);
-            if (mLastInterval != null && shard.getShardType() == Shard.ShardType.READ_INTERVAL )
-                iterator = new PlusOneFixIterator(shardGenomeLoc,new IntervalOverlapIterator(iterator,mLastInterval,false));
-            mLastInterval = shardGenomeLoc;
+            if(shard.getShardType() == Shard.ShardType.READ_INTERVAL) {
+                if (mLastInterval != null)
+                    iterator = new PlusOneFixIterator(shardGenomeLoc,new IntervalOverlapIterator(iterator,mLastInterval,false));
+                else
+                    iterator = new PlusOneFixIterator(shardGenomeLoc,iterator);
+                mLastInterval = shardGenomeLoc;                
+            }
         } else {
 
             throw new StingException("seek: Unknown shard type");
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index 87167f942..96ba4b54f 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -181,6 +181,9 @@ public abstract class SAMDataSource implements SimpleDataSource {
                                                         Double downsamplingFraction,
                                                         Boolean noValidationOfReadOrder,
                                                         Collection<SamRecordFilter> supplementalFilters) {
+        wrappedIterator = new MalformedSAMFilteringIterator(getHeader(),wrappedIterator,violations );
+        wrappedIterator = new ReadWrappingIterator(wrappedIterator);
+
         // NOTE: this (and other filtering) should be done before on-the-fly sorting
         //  as there is no reason to sort something that we will end of throwing away
         if (downsamplingFraction != null)
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index ee73a87c8..a807f5a93 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -51,9 +51,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     public void testTableRecalibrator1() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "6c59d291c37d053e0f188b762f3060a5" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "d0e902b071831bc10cc396e7e082b3c1");
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e5d9fc628dcf4f0ae115a6e6cc5423fe");
         e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7ebdce416b72679e1cf88cc9886a5edc" );
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "467c7304cd049d1629c3675fdd61fc00" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "4cd060de1e4e6d21fcd1c7a4ce7824f5" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();
@@ -81,7 +81,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testTableRecalibratorMaxQ70() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e7e6443bc4debc26e5e06b8765b60042" );
+        e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "0e2bca11d09b1b93bfc4af5c185e0d1d" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String bam = entry.getKey();