Take 2, updating picard with bug fix for bam files containing no reads.

Just stomped on the existing md5s because that's what Eric told me to do.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -309,8 +309,7 @@ public class GenomeAnalysisEngine {
      * Returns sets of samples present in the (merged) input SAM stream, grouped by readers (i.e. underlying
      * individual bam files). For instance: if GATK is run with three input bam files (three -I arguments), then the list
      * returned by this method will contain 3 elements (one for each reader), with each element being a set of sample names
-     * found in the corresponding bam file.  The sample names returned will be in order of the files passed in the input
-     * parameter list of the GATK.
+     * found in the corresponding bam file.
      *
      * @return
      */
@@ -385,7 +384,7 @@ public class GenomeAnalysisEngine {
             rg_sets.add(groups);
 
             for (SAMReadGroupRecord g : r.getFileHeader().getReadGroups()) {
-                if (hm.hasGroupIdDuplicates()) { // Check if there were read group clashes with hasGroupIdDuplicates and if so:
+                if (hm.hasReadGroupCollisions()) { // Check if there were read group clashes with hasGroupIdDuplicates and if so:
                     // use HeaderMerger to translate original read group id from the reader into the read group id in the
                     // merged stream, and save that remapped read group id to associate it with specific reader
                     groups.add(hm.getReadGroupId(r, g.getReadGroupId()));

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

@@ -235,15 +235,22 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
         final SAMRecord record = iterator.next();
         addIfNotEmpty(iterator);
 
-        if (this.samHeaderMerger.hasGroupIdDuplicates()) {
-            final String id = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
-            final String newId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), id);
-            record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newId);
+        // Fix the read group if needs be
+        if (this.samHeaderMerger.hasReadGroupCollisions()) {
+            final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.READ_GROUP_ID);
+            if (oldGroupId != null ) {
+                final String newGroupId = this.samHeaderMerger.getReadGroupId(iterator.getReader(), oldGroupId);
+                record.setAttribute(ReservedTagConstants.READ_GROUP_ID, newGroupId);
+                }
         }
-        final String oldProgramGroupId = (String) record.getAttribute(SAMTag.PG.toString());
-        if (oldProgramGroupId != null) {
-            final String newProgramGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldProgramGroupId);
-            record.setAttribute(SAMTag.PG.toString(), newProgramGroupId);
+
+        // Fix the program group if needs be
+        if (this.samHeaderMerger.hasProgramGroupCollisions()) {
+            final String oldGroupId = (String) record.getAttribute(ReservedTagConstants.PROGRAM_GROUP_ID);
+            if (oldGroupId != null ) {
+                final String newGroupId = this.samHeaderMerger.getProgramGroupId(iterator.getReader(), oldGroupId);
+                record.setAttribute(ReservedTagConstants.PROGRAM_GROUP_ID, newGroupId);
+            }
         }
 
         // if we don't have a read group, set one correctly

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1,
-                Arrays.asList("8f14c1efea00b32984ec52db7a800d1b"));
+                Arrays.asList("b7e12c4011d0043024e0dd2dd5764752"));
         executeTest("testMultiSamplePilot1", spec);
     }
 
@@ -205,7 +205,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void empirical1MbTestBinaryGeli() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseTestString() + " -L 1:10,000,000-11,000,000 -bm empirical --variant_output_format GELI_BINARY -confidence 50", 1,
-                Arrays.asList("915abf82a04fcd1842f6865501bae67c"));
+                Arrays.asList("18f175c7ccaeca57b8d412e9f4ebbe50"));
         executeTest("empirical1MbTestBinaryGeli", spec);
     }
 }

settings/repository/edu.mit.broad/picard-private-1109.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="1109" status="integration" publication="20091112172900" />
 </ivy-module>

settings/repository/net.sf/picard-1.05.140.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.05.140" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.07.168.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.07.168" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.05.140.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.05.140" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.07.168.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.07.168" status="release" />
+</ivy-module>