Revving Picard to pick up new SamFileHeaderMerger.

Updated ReadFilter abstract class to implement (via UnsupportedOperationException) the new SamRecordFilter.filterOut().
In IndelRealignerIntegrationTest updates for Picard fixes to SAMRecord.getInferredInsertSize() in svn r1115 & r1124.
- Ran FixMates to create new input BAM since running IR with variable maxReadsInMemory means all reads weren't realigned leading to different outputs.
- Updated md5s to match new expectations after looking at TLEN diff engine output.

public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.filters;
 
 import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
@@ -16,4 +17,18 @@ public abstract class ReadFilter implements SamRecordFilter {
      * @param engine the engine.
      */
     public void initialize(GenomeAnalysisEngine engine) {}
+
+
+    /**
+     * Determines whether a pair of SAMRecord matches this filter
+     *
+     * @param first  the first SAMRecord to evaluate
+     * @param second the second SAMRecord to evaluate
+     *
+     * @return true if the SAMRecords matches the filter, otherwise false
+     * @throws UnsupportedOperationException when paired filter not implemented
+     */
+    public boolean filterOut(final SAMRecord first, final SAMRecord second) {
+        throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass());
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java

@@ -9,13 +9,13 @@ import java.util.Map;
 
 public class IndelRealignerIntegrationTest extends WalkerTest {
 
-    private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.bam";
+    private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam";
     private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals";
     private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
     private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
     private static final String baseCommand = baseCommandPrefix + "-o %s ";
-    private static final String base_md5 = "e041186bca9dccf360747c89be8417ad";
-    private static final String base_md5_with_SW_or_VCF = "d7c7acd346ee4c8d34f1e2499ff7c313";
+    private static final String base_md5 = "7574ab7d0b1ee5d44a0b3f85b6e944e6";
+    private static final String base_md5_with_SW_or_VCF = "a918d69d26d3c87b29002ed31f428c48";
 
     @Test
     public void testDefaults() {
@@ -38,7 +38,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
-                Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
+                Arrays.asList("36718f10d523dfb0fa2a709480f24bd4"));
         executeTest("realigner known indels only from VCF", spec1);
     }
 
@@ -55,7 +55,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     public void testLods() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "-LOD 60", base_md5 );
-        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "f158f18198cf48bbb3d4f1b7127928a3" );
+        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "9a75a0f7ad0442c78d0f8df260e733a4" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -71,7 +71,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
                 1,
-                Arrays.asList("fe39c007d287d372a8137d11c60fbc50"));
+                Arrays.asList("e98f51d71f0a82141b36a7e9f94db237"));
         executeTest("realigner long run", spec);
     }
 
@@ -80,7 +80,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
                 1,
-                Arrays.asList("e77e59cc6363cf58f392ce5ea8d7e0b6"));
+                Arrays.asList("58ac675d0699eb236d469b8e84513d11"));
         executeTest("realigner no output tags", spec);
     }
 

settings/repository/edu.mit.broad/picard-private-parts-2375.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2181" status="integration" publication="20120110094400" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2375" status="integration" publication="20120502094400" />
 </ivy-module>

settings/repository/net.sf/picard-1.59.1066.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.59.1066" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.67.1197.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.67.1197" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.59.1066.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.59.1066" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.67.1197.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.67.1197" status="release" />
+</ivy-module>