Merge pull request #210 from broadinstitute/gda_QUAL_fix_GSA-910

Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VA...

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java

@@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9f960977b1b8d90ac75ba4306336553c");
+        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","5eabc12fc7b4f9749e6d1be0f5b45d14");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
-        executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","296917e690616682b79229ec5f923bdb");
+        executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","71b7b9eac1e4a9b2b7e8c3689d1f29ec");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "545d85ce79841f01886a5cf824a4a12c");
+        executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "fc36e925e269b035d4b27edb661be06b");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java

@@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("21d1d3c6a50006c723cec738f19caeb6"));
+                Arrays.asList("1ab95513a3abb5b760578831c61ef94b"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -120,7 +120,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("3011c20165951ca43c8a4e86a5835dbd"));
+                Arrays.asList("94bfccbd06043e90ae1b1c66fc3afe07"));
         executeTest("test mismatched PLs", spec);
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java

@@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "5954a46971b7546d30151b068cded42a");
+                "7d2cc5c4ece386beedf6b07dfbe5bf26");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "b3684c670f68f5a3a348a7fd2b25f10a");
+                "a17856f709b546eaed486841d78248d2");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "65188ec4e3b91796f62bfb5b965ccf1f");
+                "e2d32d0dce2c5502a8e877f6bbb65a10");
     }
 
     @Test

settings/repository/org.broadinstitute/variant-1.90.1446.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.90.1442" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.90.1446" status="integration" />
 </ivy-module>