Bumped picard to latest svn version.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java

@@ -184,7 +184,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
 
         record.setHeader(samHeaderMerger.getMergedHeader());
         if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() >= 0) {
-            record.setReferenceIndex(this.samHeaderMerger.getNewSequenceMapping(iterator.getReader(),record.getReferenceIndex()));
+            record.setReferenceIndex(this.samHeaderMerger.getMergedSequenceIndex(iterator.getReader(),record.getReferenceIndex()));
         }
         
         //System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());

settings/repository/edu.mit.broad/picard-private-801.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="771" status="integration" publication="20090528143800" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="801" status="integration" publication="20090102400000" />
 </ivy-module>

settings/repository/net.sf/picard-1.01.26.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.01.26" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.01.38.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.01.38" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.0.26.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.0.26" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.0.38.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.0.38" status="release" />
+</ivy-module>