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Move htsjdk to ver 2.10.0 and picard to ver 2.9.2

This commit is contained in:
Ron Levine 2017-06-01 16:36:52 -04:00
parent 3de98263f5
commit 70b2575c29
4 changed files with 13 additions and 7 deletions
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4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
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@ -204,8 +204,10 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
// No testing of MD5 here, we previously blew up due to a 0 length haplotypes, so we just need to pass // No testing of MD5 here, we previously blew up due to a 0 length haplotypes, so we just need to pass
@Test @Test
public void testHaplotype0Length() { public void testHaplotype0Length() {
final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --disableDithering -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference + " -baq CALCULATE_AS_NECESSARY -glm BOTH -o /dev/null", "-T UnifiedGenotyper --disableDithering -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference +
" -baq CALCULATE_AS_NECESSARY -glm BOTH -o " + outputVCF,
0, 0,
Collections.<String>emptyList()); Collections.<String>emptyList());
executeTest("testHaplotype0Length", spec); executeTest("testHaplotype0Length", spec);

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -297,7 +297,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void HCTestDoesNotFailOnBadRefBase() { public void HCTestDoesNotFailOnBadRefBase() {
// don't care about the output - just want to make sure it doesn't fail // don't care about the output - just want to make sure it doesn't fail
final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2"; final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o " + outputVCF + " -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2";
final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.<String>emptyList()); final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.<String>emptyList());
executeTest("HCTestDoesNotFailOnBadRefBase: ", spec); executeTest("HCTestDoesNotFailOnBadRefBase: ", spec);
} }
@ -328,9 +329,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testLeftAlignmentBamOutBugFix() throws FileNotFoundException { public void testLeftAlignmentBamOutBugFix() throws FileNotFoundException {
final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3"; final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3";
final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT) final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
+ " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef"; + " --no_cmdline_in_header -bamout %s -o " + outputVCF + " -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut)); final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut));
executeTest("LeftAlignmentBamOutBugFix", spec); executeTest("LeftAlignmentBamOutBugFix", spec);
validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(LEFT_ALIGNMENT_BAMOUT_TEST_INPUT))), md5BAMOut); validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(LEFT_ALIGNMENT_BAMOUT_TEST_INPUT))), md5BAMOut);

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
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@ -84,9 +84,11 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
} }
public void HCTestBamWriter(final HaplotypeBAMWriter.Type type, final String md5) { public void HCTestBamWriter(final HaplotypeBAMWriter.Type type, final String md5) {
final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " + "-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference +
"-bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1, " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o " + outputVCF +
" -bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1,
Arrays.asList(md5)); Arrays.asList(md5));
executeTest("HC writing bams with mode " + type, spec); executeTest("HC writing bams with mode " + type, spec);
} }

4
public/gatk-root/pom.xml
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@ -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> <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 --> <!-- Version numbers for picard and htsjdk -->
<htsjdk.version>2.9.1</htsjdk.version> <htsjdk.version>2.10.0</htsjdk.version>
<picard.version>2.9.0</picard.version> <picard.version>2.9.2</picard.version>
</properties> </properties>
<!-- Dependency configuration (versions, etc.) --> <!-- Dependency configuration (versions, etc.) -->