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Updating md5s due to changes in assembly graph creation algorithms and default parameter

This commit is contained in:
Mark DePristo 2013-03-26 22:07:25 -04:00
parent 197d149495
commit fde7d36926
2 changed files with 12 additions and 12 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -63,7 +63,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6dd29d6fec056419ab0fa03a7d43d85e");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "f9fa4d3c88fd9c0f23c7a3ddd3d24a8c");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -75,7 +75,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
// TODO -- need a better symbolic allele test
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8225fb59b9fcbe767a473c9eb8b21537");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e746a38765298acd716194aee4d93554");
}
private void HCTestComplexGGA(String bam, String args, String md5) {
@ -87,12 +87,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"84616464aed68f4d9bc9e08472eff9c0");
"e8ffbfae3c1af5be02631a31f386a431");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"e2d1023b846bfac31b4f7a3a4b90d931");
"c3a98b19efa7cb36fe5f5f2ab893ef56");
}
}

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -69,12 +69,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "9859b136d05085b5ec0833035289106a");
HCTest(CEUTRIO_BAM, "", "45856ad67bfe8d8bea45808d8258bcf1");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "27f660bf1c9a6ed7167d77022d401b73");
HCTest(NA12878_BAM, "", "b6c93325f851ac358ea49260fb11b75c");
}
@Test(enabled = false) // can't annotate the rsID's yet
@ -85,7 +85,7 @@ 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",
"e25fc2196401a16347e0c730dbcbe828");
"4ca6b560d0569cdca400d3e50915e211");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "325d7d73e0bd86b6cb146b249eda959a");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "5d06ec5502d3f157964bd7b275d6a0cb");
}
@Test
@ -111,14 +111,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("53a50dae68f0175ca3088dea1d3bb881"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ec97a0a65890169358842e765ff8dd15"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("d3bc6adde8cd9514ae5c49cd366d5de4"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -140,7 +140,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("5280f1a50ca27d8e435da0bd5b26ae93"));
Arrays.asList("4adb833ed8af20224b76bba61e2b0d93"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -148,7 +148,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
Arrays.asList("addceb63f5bfa9f11e15335d5bf641e9"));
Arrays.asList("1704b0901c86f8f597d931222d5c8dd8"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}