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Update md5s to reflect new downsampling and assembly algorithm output 

-- Only minor differences, with improvement in allele discovery where the sites differ.  The test of an insertion at the start of the MT no longer calls a 1 bp indel at position 0 in the genome
This commit is contained in:
Mark DePristo 2013-03-19 16:22:06 -04:00
parent 1fa5050faf
commit 2e36f15861
2 changed files with 13 additions and 13 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", "", "b83b53741edb07218045d6f25f20a18b");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "2b9355ab532314bce157c918c7606409");
}
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, "", "298c1af47a515ea7c8c1ea704d7755ce");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8225fb59b9fcbe767a473c9eb8b21537");
}
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",
"fd3412030628fccf77effdb1ec03dce7");
"f2add041ba1692db576ae9763a14b8a6");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"633e8930a263e34def5e097889dd9805");
"383320e81a1a3bee880fcc6cd0564452");
}
}

18
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, "", "694d6ea7f0f305854d4108379d68de75");
HCTest(CEUTRIO_BAM, "", "75dbef605b28f02616b13bb5d8bf2fbd");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "995501d8af646af3b6eaa4109e2fb4a0");
HCTest(NA12878_BAM, "", "fa8705a5d3ada66470019fa7ddcb9b2c");
}
@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",
"627124af27dc4556d83df1a04e4b9f97");
"9f9062a6eb93f984658492400102b0c7");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -96,12 +96,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "205fc8647b908c0dab7b5c6d6b78c0c2");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3a38f6fade253577d205a00db3e67828");
}
@Test
public void testHaplotypeCallerInsertionOnEdgeOfContig() {
HCTest(CEUTRIO_MT_TEST_BAM, "-dcov 90 -L MT:1-10", "e6f7bbab7cf96cbb25837b7a94bf0f82");
HCTest(CEUTRIO_MT_TEST_BAM, "-dcov 90 -L MT:1-10", "7f1fb8f9587f64643f6612ef1dd6d4ae");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -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("ccd30e226f097a40cdeebaa035a290a7"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("1e7b1bda6be5d3835ae318f2977cfbdd"));
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("f1250a8ecd404443dcca20741a74ec4f"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b6d63f558259883262ea84f339acb767"));
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("fd1b51b17f8f9c88abdf66a9372bce5a"));
Arrays.asList("5280f1a50ca27d8e435da0bd5b26ae93"));
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("d3eb900eecdafafda3170f67adff42ae"));
Arrays.asList("addceb63f5bfa9f11e15335d5bf641e9"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}