Merge pull request #581 from broadinstitute/jt_picard

Rev Picard because it's needed by another branch

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java

@@ -46,7 +46,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.picard.sam.SamPairUtil;
+import net.sf.samtools.SamPairUtil;
 import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMRecordComparator;

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java

@@ -60,8 +60,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     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 = "458588d68c8ea7e54443ea722604b265";
-    private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
+    private static final String base_md5 = "a102dd55451799e5f053c784b762087e";
+    private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d";
 
     @Test
     public void testDefaults() {
@@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
-                Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
+                Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192"));
         executeTest("realigner known indels only from VCF", spec1);
     }
 
@@ -101,7 +101,7 @@ 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",  "dea9bd14323b33348d9cf28e256415f2" );
+        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "4bf28d3c0337682d439257874377a681" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -117,7 +117,7 @@ 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("b91c0bf803247f703dc1cb6ccdc4f18f"));
+                Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe"));
         executeTest("realigner long run", spec);
     }
 
@@ -126,7 +126,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
                 1,
-                Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
+                Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d"));
         executeTest("realigner no output tags", spec);
     }
 
@@ -148,7 +148,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testMaxReadsInMemory() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11" );
+        e.put( "--maxReadsInMemory 10000", base_md5 );
         e.put( "--maxReadsInMemory 40000", base_md5 );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {

public/repo/net/sf/picard/1.110.1763/picard-1.110.1763.pom

@@ -3,23 +3,23 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>net.sf</groupId>
     <artifactId>picard</artifactId>
-    <version>1.109.1722</version>
+    <version>1.110.1763</version>
     <name>picard</name>
     <dependencies>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute</groupId>
             <artifactId>variant</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
         <dependency>
             <groupId>org.broad</groupId>
             <artifactId>tribble</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
         <!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 -->
         <dependency>

public/repo/net/sf/sam/1.110.1763/sam-1.110.1763.pom

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>net.sf</groupId>
     <artifactId>sam</artifactId>
-    <version>1.109.1722</version>
+    <version>1.110.1763</version>
     <name>sam-jdk</name>
     <dependencies>
         <dependency>

public/repo/org/broad/tribble/1.110.1763/tribble-1.110.1763.pom

@@ -3,13 +3,13 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.broad</groupId>
     <artifactId>tribble</artifactId>
-    <version>1.109.1722</version>
+    <version>1.110.1763</version>
     <name>tribble</name>
     <dependencies>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
     </dependencies>
 </project>

public/repo/org/broadinstitute/variant/1.110.1763/variant-1.110.1763.pom

@@ -3,18 +3,18 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.broadinstitute</groupId>
     <artifactId>variant</artifactId>
-    <version>1.109.1722</version>
+    <version>1.110.1763</version>
     <name>variant</name>
     <dependencies>
         <dependency>
             <groupId>org.broad</groupId>
             <artifactId>tribble</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.109.1722</version>
+            <version>1.110.1763</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>

public/sting-root/pom.xml

@@ -43,7 +43,7 @@
         <test.args>-Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit}</test.args>
 
         <!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
-        <picard.public.version>1.109.1722</picard.public.version>
+        <picard.public.version>1.110.1763</picard.public.version>
         <sam.version>${picard.public.version}</sam.version>
         <picard.version>${picard.public.version}</picard.version>
         <variant.version>${picard.public.version}</variant.version>