Merge pull request #1478 from broadinstitute/rhl_htsjdk_2.6.1_picard_2.6.0

Move htsjdk to ver 2.6.1 and picard to ver 2.6.0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java

@@ -71,11 +71,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSingleSample() {
-        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "13bfe41ef083d2716e07d35223916a4e");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "19c56b853b20ac674b6de1332043586d");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "64b4fa6cf4c4d16e822289990ee88240");
+        DTTest("testMultiSample ", "-I " + multiSample, "90770023666f3c1d6a3f35e5ecada4a8");
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -164,7 +164,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters1() {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("ced70cfb4e6681a3aa0633cd0510ada0"));
+                Arrays.asList("b6e8d70223826000ea1a6d6bc9c4fc65"));
         executeTest("test genotype filter #1", spec1);
     }
 
@@ -172,7 +172,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
     public void testGenotypeFilters2() {
         WalkerTestSpec spec2 = new WalkerTestSpec(
                 baseTestString() + " -G_filter 'isHomVar == 1' -G_filterName foo --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("837b6a3ce3fad3bd77ec3e870c4d2f10"));
+                Arrays.asList("9cd315a433ab7d9da637156011328509"));
         executeTest("test genotype filter #2", spec2);
     }
 
@@ -207,7 +207,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("260dd9d7e35737fe695b241b7a5a52a2"));
+                Arrays.asList("b0016040127766a4163fcbd91afff3ea"));
         executeTest("testFilteringDPfromFORMAT", spec);
     }
 
@@ -216,7 +216,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 10' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormatWithMissing.vcf", 1,
-                Arrays.asList("4bf46103a71bac92a11eae04b97f9877"));
+                Arrays.asList("cc55e6a7bae2ab3503ecefc973ec1c2d"));
         executeTest("testFilteringDPfromFORMATWithMissing", spec);
     }
 
@@ -225,7 +225,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --missingValuesInExpressionsShouldEvaluateAsFailing --genotypeFilterExpression 'DP < 10' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormatWithMissing.vcf", 1,
-                Arrays.asList("baeda696c92adc8745ac4ebbdead6c91"));
+                Arrays.asList("521e6f33325a051ced28152a1e7c273d"));
         executeTest("testFilteringDPfromFORMATAndFailMissing", spec);
     }
 
@@ -234,7 +234,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf --invertGenotypeFilterExpression", 1,
-                Arrays.asList("907527b89d3f819cc3f6f88f51fcaaf6"));
+                Arrays.asList("c6bc275c97a9e737748d16132ee76f48"));
         executeTest("testInvertGenotypeFilterExpression", spec);
     }
 
@@ -243,7 +243,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP >= 8' --genotypeFilterName highDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
-                Arrays.asList("d79b2e5a7502a6d6e902bc40d74cc826")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
+                Arrays.asList("9321b5993d51a4da02f69e5467164587")); // Differs from testInvertFilter because FILTER description uses the -genotypeFilterExpression argument
         executeTest("testInvertJexlGenotypeFilterExpression", spec);
     }
 
@@ -252,7 +252,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf --setFilteredGtToNocall", 1,
-                Arrays.asList("2ff3753215d418712309e50da323f6e8"));
+                Arrays.asList("00990d54017b7384ce9f979d796b9d16"));
         executeTest("testSetFilteredGtoNocall", spec);
     }
 
@@ -263,7 +263,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
                 "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
                         + " -G_filter 'GQ < 20' -G_filterName lowDP -G_filter 'DP<10' -G_filterName lowGQ -V " + privateTestDir + "variantFiltrationInfoField.vcf --setFilteredGtToNocall",
                 1,
-                Arrays.asList("3b074975bb6f70c84b2dd81695bb89ff"));
+                Arrays.asList("0f8ed3a62a53feca0c4b86671e4b53e4"));
         executeTest("testSetFilteredGtoNocallUpdateInfo", spec);
     }
 
@@ -274,7 +274,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("410c6b7bb62fc43bb41eee627670f757")
+                Arrays.asList("cb5ef9233503bebc81593e436a6de943")
         );
 
         spec.disableShadowBCF();

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -67,8 +67,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     private static final String SAMPLE_EXCLUSION_MD5 = "2e52f21e7dcc67151a51630807a4eef2";
     private static final String INVERT_SELECTION_MD5 = "26d192b868746ab14133f145ae812e7c";
-    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "f83ac0deb7a8b022d6d40a85627a71ec";
+    private static final String MAX_FILTERED_GT_SELECTION_MD5 = "66d92fac72b339195b393c9915643a14";
-    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "346620b7a5d66dabf89d3f42d6e27db7";
+    private static final String MIN_FILTERED_GT_SELECTION_MD5 = "965c0cf7daa03a1731b371bb20b582d4";
     private static final String NO_CALL_FILTERING_KEEP_ONE = "6e2401190c5ada6a3bed2640c068f43b";
     private static final String NO_CALL_FILTERING_KEEP_TWO =  "6bced1ab6a3d58f1fd905b7f601987a3";
 
@@ -744,7 +744,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("410c6b7bb62fc43bb41eee627670f757")
+                Arrays.asList("cb5ef9233503bebc81593e436a6de943")
         );
 
         spec.disableShadowBCF();
@@ -759,7 +759,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                 "-T SelectVariants --setFilteredGtToNocall --removeUnusedAlternates --excludeNonVariants -R " + b37KGReference + " --variant " +
                         testfile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("349136d92f915f8c7ba8a2f92e51d6b7"));
+                Arrays.asList("f5b2592361d8ab0d47e5047e63f78e4c"));
         executeTest("testSetFilteredGtoNocallUpdateInfo", spec);
     }
 

public/gatk-root/pom.xml

@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>2.5.0</htsjdk.version>
+        <htsjdk.version>2.6.1</htsjdk.version>
-        <picard.version>2.5.0</picard.version>
+        <picard.version>2.6.0</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java

@@ -40,8 +40,8 @@ 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 = "ab7407d2299d9ba73449cea376eeb9c4";
+    private static final String base_md5 = "12e7c9fd7af4fc9184c5f58a1660eac5";
-    private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364";
+    private static final String base_md5_with_SW_or_VCF = "2d3f79298687da007da52286b5c7261d";
 
     @Test
     public void testDefaults() {
@@ -64,7 +64,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec1 = new WalkerTestSpec(
                 baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
                 1,
-                Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30"));
+                Arrays.asList("3d028025dcb8d268262274d8ffc42635"));
         executeTest("realigner known indels only from VCF", spec1);
     }
 
@@ -81,7 +81,7 @@ 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",  "0c4597e48b4e194de32ebe494704ea6b" );
+        e.put( "-LOD 1 --consensusDeterminationModel USE_SW",  "44868da9b026201572cbfaaedacc57eb" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@@ -97,7 +97,7 @@ 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("19e6859b9ef09c7e0a79a19626908b17"));
+                Arrays.asList("c40aa32bca520015acb175fde52b4ed4"));
         executeTest("realigner long run", spec);
     }
 
@@ -106,7 +106,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
                 1,
-                Arrays.asList("8f5684359d7b26acaacfa657ef395a0c"));
+                Arrays.asList("3adc7711a163a65a570a47fe28eb4d24"));
         executeTest("realigner no output tags", spec);
     }
 
@@ -128,7 +128,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
     @Test
     public void testMaxReadsInMemory() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378");
+        e.put("--maxReadsInMemory 10000", "b8a4491506303dc96cf105ba069dd928");
         e.put( "--maxReadsInMemory 40000", base_md5 );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {