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Changes to integration tests

This commit is contained in:
Guillermo del Angel 2012-04-18 19:53:42 -04:00
parent 82efd4457e
commit 960e7e6aaf
1 changed files with 16 additions and 16 deletions
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32
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -30,7 +30,7 @@ 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("d3191b2f10139c969501990ffdf29082"));
Arrays.asList("9b08dc6800ba11bc6d9f6ccf392a60fe"));
executeTest("test MultiSample Pilot1", spec);
}
@ -54,7 +54,7 @@ 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("7c7288170c6aadae555a44e79ca5bf19"));
Arrays.asList("d275e0f75368dbff012ea8655dce3444"));
executeTest("test SingleSample Pilot2", spec);
}
@ -80,7 +80,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "2158eb918abb95225ea5372fcd9c9236";
private final static String COMPRESSED_OUTPUT_MD5 = "1e3c897794e5763a8720807686707b18";
@Test
public void testCompressedOutput() {
@ -101,7 +101,7 @@ 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 = "834e85f6af4ad4a143b913dfc7defb08";
String md5 = "06d11ed89f02f08911e100df0f7db7a4";
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,
@ -200,8 +200,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "d5879f1c277035060434d79a441b31ca" );
e.put( 1.0 / 1850, "13f80245bab2321b92d27eebd5c2fc33" );
e.put( 0.01, "d07e5ca757fbcb1c03f652f82265c2f8" );
e.put( 1.0 / 1850, "d1fb9186e6f39f2bcf5d0edacd8f7fe2" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -225,7 +225,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("8c134a6e0abcc70d2ed3216d5f8e0100"));
Arrays.asList("623be1fd8b63a01bfe35ac864d5199fe"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("34baad3177712f6cd0b476f4c578e08f"));
Arrays.asList("40ea10c0238c3be2991d31ae72476884"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("4bf4f819a39a73707cae60fe30478742"));
Arrays.asList("c9b0bd900a4ec949adfbd28909581eeb"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -278,7 +278,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("ae08fbd6b0618cf3ac1be763ed7b41ca"));
Arrays.asList("6b7c8691c527facf9884c2517d943f2f"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -291,7 +291,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("120600f2bfa3a47bd93b50f768f98d5b"));
Arrays.asList("d72603aa33a086d64d4dddfd2995552f"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -301,7 +301,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("2e75d2766235eab23091a67ea2947d13"));
Arrays.asList("4a59fe207949b7d043481d7c1b786573"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -311,7 +311,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("5057bd7d07111e8b1085064782eb6c80"));
Arrays.asList("a8a9ccf30bddee94bb1d300600794ee7"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -319,7 +319,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels() {
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("c0f9ca3ceab90ebd38cc0eec9441d71f"));
Arrays.asList("0b388936022539530f565da14d5496d3"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
@ -368,7 +368,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("53758e66e3a3188bd9c78d2329d41962"));
Arrays.asList("973178b97efd2daacc9e45c414275d59"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -376,7 +376,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("3aa39b1f6f3b1eb051765f9c21f6f461"));
Arrays.asList("220facd2eb0923515d1d8ab874055564"));
executeTest("test minIndelFraction 0.25", spec);
}