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Updated integration tests for the new adaptor clipping fix.

This commit is contained in:
Mauricio Carneiro 2011-12-30 12:50:40 -05:00
parent c7d0a9ebee
commit 55cfa76cf3
8 changed files with 57 additions and 59 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -184,12 +184,12 @@ public class ReadUtils {
* in these cases the adaptor boundary is at the start of the read plus the inferred insert size (plus one)
*
* @param read the read being tested for the adaptor boundary
* @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. NULL if the read is unmapped or the insert size cannot be determined (and is necessary for the calculation).
* @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. NULL if the read is unmapped or the mate is mapped to another contig.
*/
public static Integer getAdaptorBoundary(final SAMRecord read) {
final int insertSize = Math.abs(read.getInferredInsertSize()); // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value)
if (insertSize == 0 || read.getReadUnmappedFlag()) // no adaptors in reads with mates in another
if (insertSize == 0 || read.getReadUnmappedFlag()) // no adaptors in reads with mates in another
return null; // chromosome or unmapped pairs
int adaptorBoundary; // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read)

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

@ -29,12 +29,10 @@ 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="da2a02d02abac9de14cc4b187d8595a1";
String expected_md5="06eedc2e7927650961d99d703f4301a4";
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("ac5f409856a1b79316469733e62abb91"));
Arrays.asList("e70eb5f80c93e366dcbe3cf684c154e4"));
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("f9aa7bee5a61ac1a9187d0cf1e8af471"));
Arrays.asList("2977bb30c8b84a5f4094fe6090658561"));
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("6f27fd863b6718d59d2a2d8e2a20bcae"));
Arrays.asList("1e52761fdff73a5361b5eb0a6e5d9dad"));
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("40bbd3d5a2397a007c0e74211fb33433"));
Arrays.asList("0948cd1dba7d61f283cc4cf2a7757d92"));
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("40622d39072b298440a77ecc794116e7"));
Arrays.asList("bb4eebfaffc230cb8a31e62e7b53a300"));
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("31faae1bc588d195ff553cf6c47fabfa"));
Arrays.asList("062155edec46a8c52243475fbf3a2943"));
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 = "cd597a8dae35c226a2cb110b1c9f32d5";
final static String SUMMARY_MD5 = "ffdbd9cdcb4169ebed5ae4bec797260f";
@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("c86ac1ef404c11d5e5452e020c8f7ce9", SUMMARY_MD5));
Arrays.asList("9e4ec9c23f21a8162d27a39ab057398c", 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("d8536a55fe5f6fdb1ee6c9511082fdfd", SUMMARY_MD5));
Arrays.asList("e6044b4495ef24f542403e6a94437068", 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("bc966060184bf4605a31da7fe383464e", "d624eda8f6ed14b9251ebeec73e37867"));
Arrays.asList("4496551d4493857e5153d8172965e527", "b0667e31af9aec02eaf73ca73ec16937"));
executeTest("formatBed lots of arguments", spec);
}
}

14
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
View File

@ -61,13 +61,13 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
File baseOutputFile = this.createTempFile("depthofcoveragemapq0",".tmp");
spec.setOutputFileLocation(baseOutputFile);
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("f39af6ad99520fd4fb27b409ab0344a0",baseOutputFile);
spec.addAuxFile("6b15f5330414b6d4e2f6caea42139fa1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("cc6640d82077991dde8a2b523935cdff", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("0fb627234599c258a3fee1b2703e164a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
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"));
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"));
execute("testMapQ0Only",spec);
@ -84,7 +84,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
File baseOutputFile = this.createTempFile("testManySamples",".tmp");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("d73fa1fc492f7dcc1d75056f8c12c92a",baseOutputFile);
spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
execute("testLotsOfSamples",spec);
}

38
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -55,25 +55,25 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.setOutputFileLocation(baseOutputFile);
// now add the expected files that get generated
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"));
spec.addAuxFile("2f072fd8b41b5ac1108797f89376c797", baseOutputFile);
spec.addAuxFile("d17ac7cc0b58ba801d2b0727a363d615", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("c05190c9e6239cdb1cd486edcbc23505", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("c94a52b4e73a7995319e0b570c80d2f7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("1970a44efb7ace4e51a37f0bd2dc84d1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("c321c542be25359d2e26d45cbeb6d7ab", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("9023cc8939777d515cd2895919a99688", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("3597b69e90742c5dd7c83fbc74d079f3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("1a6ea3aa759fb154ccc4e171ebca9d02", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("b492644ff06b4ffb044d5075cd168abf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("77cef87dc4083a7b60b7a7b38b4c0bd8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("8e1adbe37b98bb2271ba13932d5c947f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("761d2f9daf2ebaf43abf65c8fd2fcd05", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("0582b4681dbc02ece2dfe2752dcfd228", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("0685214965bf1863f7ce8de2e38af060", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("7a0cd8a5ebaaa82621fd3b5aed9c32fe", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testBaseOutputNoFiltering",spec);
}

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

@ -227,7 +227,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("d87ce4b405d4f7926d1c36aee7053975"));
Arrays.asList("b11df6587e4e16cb819d76a900446946"));
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("c5989e5d67d9e5fe8c5c956f12a975da"));
Arrays.asList("59068bc8888ad5f08790946066d76602"));
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("daca0741278de32e507ad367e67753b6"));
Arrays.asList("fa4f3ee67d98b64102a8a3ec81a3bc81"));
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("0ccc4e876809566510429c64adece2c7"));
Arrays.asList("df90890e43d735573a3b3e4f289ca46b"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}

28
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -5,11 +5,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.HashMap;
import java.util.Map;
import java.util.Arrays;
import java.util.List;
import java.io.File;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class RecalibrationWalkersIntegrationTest extends WalkerTest {
static HashMap<String, String> paramsFiles = new HashMap<String, String>();
@ -32,10 +32,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "cctestdata")
public Object[][] createCCTestData() {
new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "9469d6b65880abe4e5babc1c1a69889d" );
new CCTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "ab4940a16ab990181bd8368c76b23853" );
new CCTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "17d4b8001c982a70185e344929cf3941");
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" );
new CCTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "955a8fa2ddb2b04c406766ccd9ac45cc" );
return CCTest.getTests(CCTest.class);
}
@ -89,10 +89,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@DataProvider(name = "trtestdata")
public Object[][] createTRTestData() {
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f020725d9f75ad8f1c14bfae056e250f" );
new TRTest( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
new TRTest( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "d04cf1f6df486e45226ebfbf93a188a5");
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" );
new TRTest( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "502c7df4d4923c4d078b014bf78bed34" );
return TRTest.getTests(TRTest.class);
}
@ -123,7 +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", "bd8288b1fc7629e2e8c2cf7f65fefa8f");
e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "0b88d0e8c97e83bdeee2064b6730abff");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -147,7 +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", "f020725d9f75ad8f1c14bfae056e250f" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0b7123ae9f4155484b68e4a4f96c5504" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -176,7 +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", "1f643bca090478ba68aac88db835a629" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "8379f24cf5312587a1f92c162ecc220f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -230,7 +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", "b00e99219aeafe2516c6232b7d6a0a00");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7e973328751d233653530245d404a64d");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -254,7 +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", "7b92788ce92f49415af3a75a2e4a2b33");
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "fd9e37879069aa6d84436c25e472b9e9");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -282,7 +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", "f34f7141351a5dbf9664c67260f94e96" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "828d247c6e8ef5ebdf3603dc0ce79f61" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();