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Nope, loads of integration tests had to be changed.

This commit is contained in:
Eric Banks 2012-05-07 14:30:42 -04:00
parent 66838a073e
commit c40cda7e3c
11 changed files with 27 additions and 26 deletions
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1
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
View File

@ -118,6 +118,7 @@ public class StandardVCFWriter extends IndexingVCFWriter {
}
if ( mHeader.hasGenotypingData() ) {
mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write("FORMAT");
for ( String sample : mHeader.getGenotypeSamples() ) {
mWriter.write(VCFConstants.FIELD_SEPARATOR);

4
public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java
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@ -24,7 +24,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
1,
Arrays.asList("8c44f58039ec444bc376fa732d4856dd"));
Arrays.asList("444a20659f67592a8284e0b7849e4302"));
executeTest("Test symbolic alleles", spec);
}
@ -33,7 +33,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
1,
Arrays.asList("d2fc144d5996530b9161af3d22af41d9"));
Arrays.asList("93a24c019663a6011b4d6de12538df11"));
executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -152,7 +152,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testTabixAnnotations() {
final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
final String MD5 = "bb9a148716fc69d706c5be146c1afa00";
for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -A HomopolymerRun --variant:vcf " + validationDataLocation + file + " -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf -NO_HEADER", 1,

8
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -172,7 +172,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
e.put( "-sites_only", "446ed9a72d210671ed48aa1f572b77e3" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "ecf92054c1e4bd9d6529b8002d385165" );
e.put( "--output_mode EMIT_ALL_SITES", "e10819a2a7960254e27ed2b958b45d56" );
@ -376,7 +376,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("973178b97efd2daacc9e45c414275d59"));
Arrays.asList("1e4595c85159bd9b62eff575134b5dd9"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -384,7 +384,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("220facd2eb0923515d1d8ab874055564"));
Arrays.asList("6d9dbb949626fdb0bca6a7904e9b0c1f"));
executeTest("test minIndelFraction 0.25", spec);
}
@ -392,7 +392,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction100() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 1", 1,
Arrays.asList("50fe9a4c5633f6395b45d9ec1e00d56a"));
Arrays.asList("a31a355bc2b8257b2a45494e97322694"));
executeTest("test minIndelFraction 1.0", spec);
}
}

10
public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java
View File

@ -33,7 +33,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqUnif + "--variant " + testfile),
1,
Arrays.asList("d49baeb8000a426c172ce1d81eb37963")
Arrays.asList("6a9e990a9252840904b5144213915b32")
);
executeTest("testNoSampleSelectionFreqUniform--" + testfile, spec);
@ -45,7 +45,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleNone + freqAF + "--variant " + testfile),
1,
Arrays.asList("0fb0d015d462c34514fc7e96beea5f56")
Arrays.asList("eaa2385086cddff68cf4fdb81cbdbbb9")
);
executeTest("testNoSampleSelectionFreqAF--" + testfile, spec);
@ -57,7 +57,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqUnif + "--variant " + testfile),
1,
Arrays.asList("0672854299d42ea8af906976a3849ae6")
Arrays.asList("24077656f590d6905546f7e019c8dccb")
);
executeTest("testPolyGTFreqUniform--" + testfile, spec);
@ -69,7 +69,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGT + freqAF + "--variant " + testfile),
1,
Arrays.asList("5bdffda1a063d0bddd6b236854ec627d")
Arrays.asList("3c1180fd9b5e80e540b39c5a95fbe722")
);
executeTest("testPolyGTFreqAF--" + testfile, spec);
@ -81,7 +81,7 @@ public class ValidationSiteSelectorIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(sampleGL + freqAF + "--variant " + testfile),
1,
Arrays.asList("35ef16aa41303606a4b94f7b88bd9aa8")
Arrays.asList("ad30c028864348204ebe80b9c8c503e8")
);
executeTest("testPolyGLFreqAF--" + testfile, spec);

10
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -27,8 +27,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"0ddd1e0e483d2eaf56004615cea23ec7", // tranches
"f8e21a1987960b950db1f0d98be45352", // recal file
"f67d844b6252a55452cf4167b77530b1"); // cut VCF
"a45a78de049cfe767ce23d3423f80b01", // recal file
"1050c387d170639f8cec221e5dddd626"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
@ -74,8 +74,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
"da4458d05f6396f5c4ab96f274e5ccdc", // tranches
"cf380d9b0ae04c8918be8425f82035b4", // recal file
"b00e5e5a6807df8ed1682317948e8a6d"); // cut VCF
"918a5ecad5a2a8a46795144366683188", // recal file
"bf0e8ed5e250d52f0545074c61217d16"); // cut VCF
@DataProvider(name = "VRIndelTest")
public Object[][] createData2() {
@ -131,7 +131,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -o %s" +
" -tranchesFile " + validationDataLocation + "VQSR.mixedTest.tranches" +
" -recalFile " + validationDataLocation + "VQSR.mixedTest.recal",
Arrays.asList("08060b7f5c9cf3bb1692b50c58fd5a4b"));
Arrays.asList("9039576b63728df7ee2c881817c0e9eb"));
executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
}
}

10
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -96,8 +96,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "63fc20d6223e1387563a1164987d716c"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "917b5cb759afd27bce86a59d8355e85c"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "1b3a7f7ba51636173c33a56fefe7c0fe"); }
@Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "5c60eb8d5d4b957a0cf52ca008f021ba"); }
@Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "774b43e69cc7ec93090b4f6e9f4a1079"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
@ -129,15 +129,15 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void complexTestFull() { combineComplexSites("", "dd805f6edfc3cf724512dfbbe8df5183"); }
@Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "14a205edb022f79abf1863588cfee56b"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "76fdd2acc8f80eb4f9372f542673a8e2"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "76fdd2acc8f80eb4f9372f542673a8e2"); }
@Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "e118d04d1d47c02ad38c046561a9f616"); }
@Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "e118d04d1d47c02ad38c046561a9f616"); }
@Test
public void combineDBSNPDuplicateSites() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T CombineVariants -NO_HEADER -L 1:902000-903000 -o %s -R " + b37KGReference + " -V:v1 " + b37dbSNP132,
1,
Arrays.asList("ac59209efa4b21feda6493e397932f07"));
Arrays.asList("a838dc241cf357466cd4331fd298c73a"));
executeTest("combineDBSNPDuplicateSites:", spec);
}
}

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

@ -40,7 +40,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER",
1,
Arrays.asList("158b1d71b28c52e2789f164500b53732"));
Arrays.asList("8e0991576518823b339a4e2f83299d4f"));
executeTest("test left alignment", spec);
}
}

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

@ -136,7 +136,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("20b52c96f5c48258494d072752b53693")
Arrays.asList("ffa2524380d84a870d2e4a33d9f3d31a")
);
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);

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

@ -19,7 +19,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test
public void testVariantsToVCFUsingDbsnpInput() {
List<String> md5 = new ArrayList<String>();
md5.add("d64942fed2a5b7b407f9537dd2b4832e");
md5.add("a26afcce2a89f905a49c3d09719586b2");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +

2
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
View File

@ -35,7 +35,7 @@ public class VCFIntegrationTest extends WalkerTest {
String baseCommand = "-R " + b37KGReference + " -NO_HEADER -o %s ";
String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("76075307afd26b4db6234795d9fb3c2f"));
WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("acee3b6bdb4b759992f54065c675a249"));
executeTest("Test reading and writing breakpoint VCF", spec1);
}