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Updated IntegrationTests with new adaptor clipper 

phew!
This commit is contained in:
Mauricio Carneiro 2011-12-20 17:44:21 -05:00
parent cadff40247
commit 731a463415
8 changed files with 69 additions and 77 deletions
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5
public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
View File

@ -29,9 +29,12 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
+ "-R " + hg18Reference
+ " -show_indels -o %s";
String expected_md5="06eedc2e7927650961d99d703f4301a4";
String expected_md5="da2a02d02abac9de14cc4b187d8595a1";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
// before Adaptor clipping
// String expected_md5="06eedc2e7927650961d99d703f4301a4";
}
}

12
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("fbb656369eaa48153d127bd12db59d8f"));
Arrays.asList("ac5f409856a1b79316469733e62abb91"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("2977bb30c8b84a5f4094fe6090658561"));
Arrays.asList("f9aa7bee5a61ac1a9187d0cf1e8af471"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("42dd979a0a931c18dc9be40308bac321"));
Arrays.asList("6f27fd863b6718d59d2a2d8e2a20bcae"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92"));
Arrays.asList("40bbd3d5a2397a007c0e74211fb33433"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testExcludeAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("477eac07989593b58bb361f3429c085a"));
Arrays.asList("40622d39072b298440a77ecc794116e7"));
executeTest("test exclude annotations", spec);
}
@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("062155edec46a8c52243475fbf3a2943"));
Arrays.asList("31faae1bc588d195ff553cf6c47fabfa"));
executeTest("test overwriting header", spec);
}

8
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
View File

@ -32,13 +32,13 @@ import java.util.Arrays;
public class CallableLociWalkerIntegrationTest extends WalkerTest {
final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s";
final static String SUMMARY_MD5 = "ed4c255bb78313b8e7982127caf3d6c4";
final static String SUMMARY_MD5 = "cd597a8dae35c226a2cb110b1c9f32d5";
@Test
public void testCallableLociWalkerBed() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("884c9c2d96419d990a708d2bd98fcefa", SUMMARY_MD5));
Arrays.asList("c86ac1ef404c11d5e5452e020c8f7ce9", SUMMARY_MD5));
executeTest("formatBed", spec);
}
@ -46,7 +46,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalkerPerBase() {
String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("fb4524f8b3b213060c0c5b85362b5902", SUMMARY_MD5));
Arrays.asList("d8536a55fe5f6fdb1ee6c9511082fdfd", SUMMARY_MD5));
executeTest("format_state_per_base", spec);
}
@ -62,7 +62,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
public void testCallableLociWalker3() {
String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
Arrays.asList("86bd1a5f79356b3656412c4b1c60709a", "6fefb144a60b89c27293ce5ca6e10e6a"));
Arrays.asList("bc966060184bf4605a31da7fe383464e", "d624eda8f6ed14b9251ebeec73e37867"));
executeTest("formatBed lots of arguments", spec);
}
}

15
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
View File

@ -61,13 +61,14 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("5b6c16a1c667c844882e9dce71454fc4",baseOutputFile);
spec.addAuxFile("fc161ec1b61dc67bc6a5ce36cb2d02c9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("89321bbfb76a4e1edc0905d50503ba1f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("cb73a0fa0cee50f1fb8f249315d38128", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("347b47ef73fbd4e277704ddbd7834f69", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("4ec920335d4b9573f695c39d62748089", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
spec.addAuxFile("4dd16b659065e331ed4bd3ab0dae6c1b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("2be0c18b501f4a3d8c5e5f99738b4713", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("5a26ef61f586f58310812580ce842462", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testMapQ0Only",spec);
}
@ -83,7 +84,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
File baseOutputFile = this.createTempFile("testManySamples",".tmp");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
spec.addAuxFile("d73fa1fc492f7dcc1d75056f8c12c92a",baseOutputFile);
execute("testLotsOfSamples",spec);
}

40
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -55,26 +55,26 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.setOutputFileLocation(baseOutputFile);
// now add the expected files that get generated
spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("229b9b5bc2141c86dbc69c8acc9eba6a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("471c34ad2e4f7228efd20702d5941ba9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("9667c77284c2c08e647b162d0e9652d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("5a96c75f96d6fa6ee617451d731dae37", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("2aae346204c5f15517158da8e61a6c16", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("e70952f241eebb9b5448f2e7cb288131", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("054ed1e184f46d6a170dc9bf6524270c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("a395dafde101971d2b9e5ddb6cd4b7d0", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("e013cb5b11b0321a81c8dbd7c1863787", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("661160f571def8c323345b5859cfb9da", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("c95a7a6840334cadd0e520939615c77b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
spec.addAuxFile("19e862f7ed3de97f2569803f766b7433", baseOutputFile);
spec.addAuxFile("c64cc5636d4880b80b71169ed1832cd7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("1a8ba07a60e55f9fdadc89d00b1f3394", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("0075cead73a901e3a9d07c5d9c2b75f4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("d757be2f953f893e66eff1ef1f0fff4e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("de08996729c774590d6a4954c906fe84", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("58ad39b100d1f2af7d119f28ba626bfd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("0b4ce6059e6587ae5a986afbbcc7d783", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("adc2b2babcdd72a843878acf2d510ca7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("884281c139241c5db3c9f90e8684d084", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("b90636cad74ff4f6b9ff9a596e145bd6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("ad540b355ef90c566bebaeabd70026d2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("27fe09a02a5b381e0ed633587c0f4b23", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("5fcd53b4bd167b5e6d5f92329cf8678e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("7a2a19e54f73a8e07de2f020f1f913dd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("852a079c5e9e93e7daad31fd6a9f4a49", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("0828762842103edfaf115ef4e50809c6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("5c5aeb28419bba1decb17f8a166777f2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("e5fd6216b3d6a751f3a90677b4e5bf3c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testBaseOutputNoFiltering",spec);
}

22
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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("a2d3839c4ebb390b0012d495e4e53b3a"));
Arrays.asList("66ed60c6c1190754abd8a0a9d1d8d61e"));
executeTest("test MultiSample Pilot1", spec);
}
@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "d971d392956aea69c3707da64d24485b" );
e.put( "--output_mode EMIT_ALL_SITES", "21993e71ca1a06a0d1f11d58e3cc26c3" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "42e4ea7878ef8d96215accb3ba4e97b7" );
e.put( "--output_mode EMIT_ALL_SITES", "e0443c720149647469f2a2f3fb73942f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -189,7 +189,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("f0fbe472f155baf594b1eeb58166edef"));
Arrays.asList("2b2729414ae855d390e7940956745bce"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -208,7 +208,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("8c87c749a7bb5a76ed8504d4ec254272"));
Arrays.asList("95c6120efb92e5a325a5cec7d77c2dab"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -227,7 +227,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("a64d2e65b5927260e4ce0d948760cc5c"));
Arrays.asList("d87ce4b405d4f7926d1c36aee7053975"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -255,7 +255,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("69107157632714150fc068d412e31939"));
Arrays.asList("c5989e5d67d9e5fe8c5c956f12a975da"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -265,7 +265,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = 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("4ffda07590e06d58ed867ae326d74b2d"));
Arrays.asList("daca0741278de32e507ad367e67753b6"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
}
@ -275,7 +275,7 @@ 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("45633d905136c86e9d3f90ce613255e5"));
Arrays.asList("0ccc4e876809566510429c64adece2c7"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}
@ -285,7 +285,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
Arrays.asList("8bd5028cf294850b8a95b3c0af23d728"));
Arrays.asList("cff6dd0f4eb1ef0b6fc476da6ffead19"));
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
}
@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
Arrays.asList("814dcd66950635a870602d90a1618cce"));
Arrays.asList("1e2a4aab26e9ab0dae709d33a669e036"));
executeTest("test MultiSample Phase1 indels with complicated records", spec4);
}

30
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -31,10 +31,11 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "cctestdata")
public Object[][] createCCTestData() {
new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "5a52b00d9794d27af723bcf93366681e" );
new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9469d6b65880abe4e5babc1c1a69889d" );
new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941");
new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "714e65d6cb51ae32221a77ce84cbbcdc" );
new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "64e9f17a1cf6fc04c1f2717c2d2eca67" );
new CCTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "36c0c467b6245c2c6c4e9c956443a154" );
new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "ed15f8bf03bb2ea9b7c26844be829c0d" );
return CCTest.getTests(CCTest.class);
}
@ -88,10 +89,11 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "trtestdata")
public Object[][] createTRTestData() {
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" );
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" );
new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5");
new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "74314e5562c1a65547bb0edaacffe602" );
new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "2a37c6001826bfabf87063b1dfcf594f" );
new TRTest( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b2f4757bc47cf23bd9a09f756c250787" );
new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "313a21a8a88e3460b6e71ec5ffc50f0f" );
return TRTest.getTests(TRTest.class);
}
@ -121,7 +123,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesUseOriginalQuals() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "278846c55d97bd9812b758468a83f559");
e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "bd8288b1fc7629e2e8c2cf7f65fefa8f");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -145,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "2864f231fab7030377f3c8826796e48f" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -174,7 +176,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "8379f24cf5312587a1f92c162ecc220f" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1f643bca090478ba68aac88db835a629" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -200,7 +202,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "2ad4c17ac3ed380071137e4e53a398a5" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "613fb2bbe01af8cbe6a188a10c1582ca" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -228,7 +230,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesBED() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b460478d9683e827784e42bc352db8bb");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "b00e99219aeafe2516c6232b7d6a0a00");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -252,7 +254,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesVCFPlusDBsnp() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9131d96f39badbf9753653f55b148012");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b92788ce92f49415af3a75a2e4a2b33");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -280,7 +282,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "8993d32df5cb66c7149f59eccbd57f4c" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "f34f7141351a5dbf9664c67260f94e96" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -306,7 +308,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "5f913c98ca99754902e9d34f99df468f" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "13c83656567cee9e93bda9874ee80234" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();

14
public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java
View File

@ -33,20 +33,6 @@ public class ReadUtilsUnitTest extends BaseTest {
reducedRead.setAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, REDUCED_READ_COUNTS_TAG);
}
private void testReadBasesAndQuals(GATKSAMRecord read, int expectedStart, int expectedStop) {
SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null);
String expectedBases = BASES.substring(expectedStart, expectedStop);
String expectedQuals = QUALS.substring(expectedStart, expectedStop);
Assert.assertEquals(clipped.getReadBases(), expectedBases.getBytes(), "Clipped bases not those expected");
Assert.assertEquals(clipped.getBaseQualityString(), expectedQuals, "Clipped quals not those expected");
}
@Test public void testNoClip() { testReadBasesAndQuals(read, 0, 4); }
@Test public void testClip1Front() { testReadBasesAndQuals(read, 1, 4); }
@Test public void testClip2Front() { testReadBasesAndQuals(read, 2, 4); }
@Test public void testClip1Back() { testReadBasesAndQuals(read, 0, 3); }
@Test public void testClip2Back() { testReadBasesAndQuals(read, 0, 2); }
@Test
public void testReducedReads() {
Assert.assertFalse(read.isReducedRead(), "isReducedRead is false for normal read");