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Updating integration tests for minor changes due to switching to EXACT_INDEPENDENT model by default

This commit is contained in:
Mark DePristo 2012-10-21 08:10:43 -04:00
parent 6b6caf8e3a
commit d21e42608a
5 changed files with 32 additions and 32 deletions
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6
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -60,12 +60,12 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","67dabdbf1e6ed8a83d2e85766558a20a");
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","9ce24f4ff787aed9d3754519a60ef49f");
}
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","d4bfae27f1b07923f381d708d8a34cf4");
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","492c8ba9a80a902097ff15bbeb031592");
}
@Test(enabled = true)
@ -80,7 +80,7 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","da84bf45f7080a46a7a78542b3a0629d");
PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","0a8c3b06243040b743dd90d497bb3f83");
}
@Test(enabled = true)

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "75013fa6a884104f0b1797502b636698");
HCTest(CEUTRIO_BAM, "", "ee866a8694a6f6c77242041275350ab9");
}
@Test
@ -31,7 +31,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "3cd3363976b1937d801f9f82996f4abe");
HCTest(CEUTRIO_BAM, "--max_alternate_alleles_for_indels 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "53caa950535749f99d3c5b9bb61c7b60");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -53,7 +53,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "6eb9c1026225b38ba7bd3c4c218f8269");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "b4ea70a446e4782bd3700ca14dd726ff");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -64,7 +64,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "98d82d74e8d6a778290bee6c0df6d092");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "2581e760279291a3901a506d060bfac8");
}
@Test

44
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -28,7 +28,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("b3abf320f7d02d0e3b2883833419130e"));
Arrays.asList("847605f4efafef89529fe0e496315edd"));
executeTest("test MultiSample Pilot1", spec);
}
@ -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("57e409dbb12e0d85cd8af73db221b1fc"));
Arrays.asList("afb8768f31ab57eb43f75c1115eadc99"));
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 " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("48b4f4b05461be276bffc91350f08cbc"));
Arrays.asList("73c9b926c5e971a113de347a64fdcf20"));
executeTest("test Multiple SNP alleles", 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("04affcc9d720ee17bc221759707e0cd2"));
Arrays.asList("7f8d13690cb7d4173787afa00c496f12"));
executeTest("test reverse trim", spec);
}
@ -84,7 +84,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMismatchedPLs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
Arrays.asList("112e7bedfd284d4d9390aa006118c733"));
Arrays.asList("3c006b06b17bbe8e787d64eff6a63a19"));
executeTest("test mismatched PLs", spec);
}
@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "367c0355b4e7b10c2988e5c41f44b3d2";
private final static String COMPRESSED_OUTPUT_MD5 = "fd236bd635d514e4214d364f45ec4d10";
@Test
public void testCompressedOutput() {
@ -115,7 +115,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "360d1274c1072a1ae9868e4e106c2650";
String md5 = "d408b4661b820ed86272415b8ea08780";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinBaseQualityScore() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
Arrays.asList("6ae4a219c7b9c837fcbf12edeeac3c0c"));
Arrays.asList("839ecd30d354a36b5dfa2b5e99859765"));
executeTest("test min_base_quality_score 26", spec);
}
@ -182,12 +182,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "8800c58715c2bb434b69e1873cb77de6");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "67739a3ccf30975bcaef8a563e4b80cf");
testOutputParameters("--output_mode EMIT_ALL_SITES", "639df9f4c029792ac2e46069efc82b20");
}
private void testOutputParameters(final String args, final String md5) {
@ -220,12 +220,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testHeterozyosity1() {
testHeterozosity( 0.01, "f1c4c8e701b2334bf3c4f12fc395fec8" );
testHeterozosity( 0.01, "986923de51c71635d47e3d06fe3794a1" );
}
@Test
public void testHeterozyosity2() {
testHeterozosity( 1.0 / 1850, "7fbbf4a21d6bf0026bfdadbb3c086fbe" );
testHeterozosity( 1.0 / 1850, "fb12b1553f813004a394a391a8540873" );
}
private void testHeterozosity(final double arg, final String md5) {
@ -268,7 +268,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("950fb032cc9902ae48bd21f272d2fd52"));
Arrays.asList("98058fc913b61c22d44875da1f5ea89c"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -287,7 +287,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("b3df138254ed141b61a758df87757e0d"));
Arrays.asList("650c53774afacfc07a595675e8cdde17"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -302,7 +302,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("63fd9488daadd4baaef0a98f02916996"));
Arrays.asList("6a0c2a3a7bcc56ad01428c71408055aa"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -315,7 +315,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("52b5a432092995c92fe71e1942689ba8"));
Arrays.asList("5f2721c3323de5390d2d47446139f32b"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -343,13 +343,13 @@ 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("863ee56b3594f09795644127f2f9539f"));
Arrays.asList("a4761d7f25e7a62f34494801c98a0da7"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("503ca1b75cc7b2679eaa80f7b5e7ef1c"));
Arrays.asList("c526c234947482d1cd2ffc5102083a08"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -371,7 +371,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 20:10,000,000-10,100,000",
1,
Arrays.asList("945a2f994eaced8efdf8de24b58f2680"));
Arrays.asList("1e0d2c15546c3b0959b00ffb75488b56"));
executeTest(String.format("test UG with base indel quality scores"), spec);
}
@ -449,18 +449,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
Arrays.asList("da9c05f87bd6415e97f90c49cf68ed19"));
executeTest("test calling on a ReducedRead BAM", spec);
}
@Test
public void testReducedBamSNPs() {
testReducedCalling("SNP", "");
testReducedCalling("SNP", "1d4a826b144723ff0766c36aa0239287");
}
@Test
public void testReducedBamINDELs() {
testReducedCalling("INDEL", "");
testReducedCalling("INDEL", "68ef51d5c98480e0c0192e0eecb95bca");
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -190,7 +190,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("549321a2543608f214ab4893ab478be6")
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
);
executeTest("testRegenotype--" + testFile, spec);
@ -216,7 +216,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("549321a2543608f214ab4893ab478be6")
Arrays.asList("46ff472fc7ef6734ad01170028d5924a")
);
executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);

2
public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
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@ -21,7 +21,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest {
for ( final int nct : Arrays.asList(1, 2) ) {
// tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
//// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
tests.add(new Object[]{ "BOTH", "8cad82c3a5f5b932042933f136663c8a", nt, nct });
tests.add(new Object[]{ "BOTH", "85fc5d6dfeb60ed89763470f4b4c981e", nt, nct });
}
return tests.toArray(new Object[][]{});