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Updating MD5s for inclusion of RPA field header

This commit is contained in:
Mark DePristo 2012-06-15 15:53:54 -04:00
parent d015a5738d
commit 0c8b830db7
4 changed files with 24 additions and 24 deletions
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2
public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
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@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"--beagleR2:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
"--beagleProbs:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
"--beaglePhased:beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
"-L 20:1-70000 -o %s --no_cmdline_in_header ",1,Arrays.asList("8c05bda0630155bcd0ebaf155ed5e491"));
"-L 20:1-70000 -o %s --no_cmdline_in_header ",1,Arrays.asList("fbbbebfda35bab3f6f62eea2f0be1c01"));
executeTest("testBeagleChangesSitesToRef",spec);
}

42
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -36,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("c09dfbfc5b76acacb616730eaa83a150"));
Arrays.asList("f9f2912c63e3253495702099bde5de0f"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
}
@ -52,7 +52,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("0a085eac119c91d63fdd4a7e9a5e45af"));
Arrays.asList("bd7d25f6c6142837e3bc4c0d5dced2ed"));
executeTest("test SingleSample Pilot2", spec);
}
@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + testDir + "multiallelic.snps.bam -o %s -L " + testDir + "multiallelic.snps.intervals", 1,
Arrays.asList("bdbb67743c9f75ac60d0a10f94856361"));
Arrays.asList("dba580e8b5e96a28d673b437b4da1c70"));
executeTest("test Multiple SNP alleles", spec);
}
@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testBadRead() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + testDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
Arrays.asList("bf60763a6e9c9d3987cfbac43b941a48"));
Arrays.asList("174905e2547e94c3eee07ce84497692b"));
executeTest("test bad read", spec);
}
@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("1e991a6a7288be7ac603ef6467fb1ac2"));
Arrays.asList("29b15e2017b13e6cb3ad56cc74c719e7"));
executeTest("test reverse trim", spec);
}
@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "3136826ec99366b0285b278aba35cec1";
private final static String COMPRESSED_OUTPUT_MD5 = "6f14394e90fdacd29390a1f3521f5ca8";
@Test
public void testCompressedOutput() {
@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSLOD() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("fe4a96f0049edd466c030def4c62a224"));
Arrays.asList("3712dd35b0e630977c8c5226ccc532ae"));
executeTest("test SLOD", spec);
}
@ -155,7 +155,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testNDA() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("ca8d0d91fd0cef93d4a606dec84a7986"));
Arrays.asList("8a5bb0cca3004848dbca9c08fc2afed9"));
executeTest("test NDA", spec);
}
@ -163,7 +163,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testCompTrack() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
Arrays.asList("7c3518d356c05c6b9a8918357c260bfe"));
Arrays.asList("9863ecd2576c7a962f9d05a7dc670169"));
executeTest("test using comp track", spec);
}
@ -193,7 +193,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("a19c6195211b0ff036c746c7e11490ed"));
Arrays.asList("afdba62ff773ee77dd5ec947f7cf280f"));
executeTest("test confidence 1", spec1);
}
@ -201,7 +201,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence2() {
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
Arrays.asList("3fc3c36edaac133b4c11b20a5af915c4"));
Arrays.asList("d81007a1718d2e16c2d8cd5bbc0d7bf3"));
executeTest("test confidence 2", spec2);
}
@ -212,12 +212,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "82caf6c25d3aeabf7978016474e04fd0" );
testHeterozosity( 0.01, "7f3fcbe491284b321d6b92ef197644c3" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "d2a7ba1fa2d1a4153f685f3b3f6d55a2" );
testHeterozosity( 1.0 / 1850, "04d970a174dcfaccab58f2943326251d" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -241,7 +241,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("b574087efc5b259f69c429f1f415da0a"));
Arrays.asList("ba5b511efd3d99575620f14ba2ba259e"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("1b9556725b6a2cb52ad6745e9eca37e6"));
Arrays.asList("4c71fbe45faf6e2b7da0eb8ae9dd0c0f"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("9388a1216957c4722fe54af06a05f242"));
Arrays.asList("e6c116225319f505d680beeeb2063bf1"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("8f942000baaf522fcea29691fe5ef75d"));
Arrays.asList("d46e1f465c649927fb3c4ec85df35d09"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -307,7 +307,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("4b8822ccc9ac04bee37bf0c9922108f9"));
Arrays.asList("0b9d7998f222e55e82c1a7022d62a508"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + testDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("13160041d8ebfb2080981f89e39eeb4f"));
Arrays.asList("9bd02b2c648695138f2645e955bf4d8d"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -335,7 +335,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels1() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("eaef9cc984a95b5ccb4c4c1f7c20c235"));
Arrays.asList("e84f82e12deb9773dae21595b3531a07"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
@ -392,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("a3741b9de95e5858640220d62a0d318c"));
Arrays.asList("59c8f66eadd45c56f09291bf64f611e1"));
executeTest("test minIndelFraction 0.25", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+ " -L chr20:652810-681757",
1,
Arrays.asList("61a7d05f9eb4317cf0e6937d72e1e7ec"));
Arrays.asList("94f2fc24c3ac1ddbecb2e0bf7ed1597c"));
executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --no_cmdline_in_header " +
" -o %s",
1,
Arrays.asList("b532a20b5af4e8ea7a073888976c71ba")
Arrays.asList("6248c072f9a9eafe9d386d2834e94f03")
);
executeTest("testSimpleVCFStreaming", spec);