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Updated md5's from previous checkin

This commit is contained in:
Guillermo del Angel 2011-06-29 13:37:15 -04:00
parent 5b6d279a2e
commit f736a1d61b
2 changed files with 25 additions and 25 deletions
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48
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("a604a64252a8538b7d13f52bd068f797"));
Arrays.asList("258e1954e6ae55c89abc6a716e19cbe0"));
executeTest("test MultiSample Pilot1", spec);
}
@ -54,12 +54,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testWithAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("5844eda3596732a16c8559f5bfbe1723"));
Arrays.asList("edeb1db288a24baff59575ceedd94243"));
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
Arrays.asList("db4664a1785c4efb4cd9057478aa846f"));
Arrays.asList("581990130d90071b084024f4cd7caf91"));
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
}
@ -67,7 +67,7 @@ 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("36c70ec27a25f88fe2364bba2f961843"));
Arrays.asList("d120db27d694a6da32367cc4fb5770fa"));
executeTest("test SingleSample Pilot2", spec);
}
@ -77,7 +77,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "212eab2024903997625ba98009063226";
private final static String COMPRESSED_OUTPUT_MD5 = "75e5c430ed39f79f24e375037a388dc4";
@Test
public void testCompressedOutput() {
@ -107,7 +107,7 @@ 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 = "f83a33a1ecc350cae0c002e4a43a7861";
String md5 = "a29615dd37222a11b8dadd341b53e43c";
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,
@ -138,9 +138,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testCallingParameters() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--min_base_quality_score 26", "d10d0be159d80e22b9c81970ee098daf" );
e.put( "--min_mapping_quality_score 26", "f76099c403b60b6045a0ae7d9f589dc4" );
e.put( "--p_nonref_model GRID_SEARCH", "cda395fdf7352e07537610f52a6d0cdc" );
e.put( "--min_base_quality_score 26", "93e6269e38db9bc1732555e9969e3648" );
e.put( "--min_mapping_quality_score 26", "64be99183c100caed4aa5f8bad64c7e9" );
e.put( "--p_nonref_model GRID_SEARCH", "0592fe33f705ad8e2f13619fcf157805" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -153,9 +153,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "9b85d9c10d634315d20aefa565dbab60" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "245abbb39de43e89f63918a6771c0c14" );
e.put( "--output_mode EMIT_ALL_SITES", "fb7a59b318ecdb46fd96024be7e41e0e" );
e.put( "-sites_only", "1483e637dc0279935a7f90d136d147bb" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "adcd91bc7dae8020df8caf1a30060e98" );
e.put( "--output_mode EMIT_ALL_SITES", "b708acc2fa40f336bcd2d0c70091e07e" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -169,12 +169,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = 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 -stand_call_conf 10 ", 1,
Arrays.asList("f76099c403b60b6045a0ae7d9f589dc4"));
Arrays.asList("64be99183c100caed4aa5f8bad64c7e9"));
executeTest("test confidence 1", spec1);
WalkerTest.WalkerTestSpec spec2 = 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 -stand_emit_conf 10 ", 1,
Arrays.asList("879e5ab09bd0d37e0300dd34ec09db81"));
Arrays.asList("e76ca54232d02f0d92730e1affeb804e"));
executeTest("test confidence 2", spec2);
}
@ -186,8 +186,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "c7123f7b84b402f4959db950326afc13" );
e.put( 1.0 / 1850, "75e6043a68265ab6deb284bb753801f9" );
e.put( 0.01, "18d37f7f107853b5e32c757b4e143205" );
e.put( 1.0 / 1850, "2bcb90ce2f7542bf590f7612018fae8e" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -211,7 +211,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("3f45b2af75123e48b89fa1759c444ec0"));
Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -230,7 +230,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("cede928592575e617f1323866348c256"));
Arrays.asList("0919ab7e513c377610e23a67d33608fa"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq OFF",
1,
Arrays.asList("3f45b2af75123e48b89fa1759c444ec0"));
Arrays.asList("825f05b31b5bb7e82231a15c7e4e2b0d"));
executeTest(String.format("test calling with BAQ OFF"), spec);
}
@ -263,7 +263,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("7fe14d81f12d5d57e3a522b2a4f07fc6"));
Arrays.asList("cb37348c41b8181be829912730f747e1"));
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("a7da8acce1957334619f3dfeac3d1379"));
Arrays.asList("ca5b6a5fb53ae401b146cc3044f454f2"));
executeTest(String.format("test indel caller in SLX witn 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("234b6c336890cc6d9a495bc40f09d126"));
Arrays.asList("ca4343a4ab6d3cce94ce61d7d1910f81"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -301,14 +301,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("9e342e3b73ae4887620195417e1af44a"));
Arrays.asList("3f555b53e9dd14cf7cdf96c24e322364"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("f265726403ca3f28518cb4290b7bee84"));
Arrays.asList("1b9764b783acf7822edc58e6822eef5b"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
}

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

@ -40,7 +40,7 @@ public class BatchMergeIntegrationTest extends WalkerTest {
+ " -B:alleles,VCF " + alleles
+ " -I " + bam,
1,
Arrays.asList("b7839064dc4979400af4792460d9884b"));
Arrays.asList("f4ed8f4ef2cba96823c06e90e9d0de35"));
executeTest("testBatchMerge UG genotype given alleles:" + new File(bam).getName() + " with " + new File(alleles).getName(), spec);
}
}