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Added several integration tests for UG indel caller: 

- Basic
- Multiple technology
- Test minIndelCnt parameter

Added also 2 disabled tests:
- Parallelization: issue w/code right now is that if -nt > 1, filter field shows "PASS" instead to ".", cause TBD
- Genotype given alleles mode: code not working yet.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5404 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-03-08 16:21:21 +00:00
parent 77fe902dbd
commit 00ac51acc8
1 changed files with 95 additions and 0 deletions
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95
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -186,6 +186,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
}
}
// --------------------------------------------------------------------------------------------------------------
//
// testing calls with SLX, 454, and SOLID data
@ -203,4 +204,98 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest(String.format("test multiple technologies"), spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing indel caller
//
// --------------------------------------------------------------------------------------------------------------
// Basic indel testing with SLX data
@Test
public void testSimpleIndels() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand +
" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" +
" -o %s" +
" -glm DINDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("a595df10d47a1fa7b2e1df2cd66d7ff0"));
executeTest(String.format("test indel caller in SLX"), spec);
}
// Basic indel testing with SLX data
@Test
public void testIndelsWithLowMinAlleleCnt() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand +
" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" +
" -o %s" +
" -glm DINDEL -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("e65e7be8bf736a39d86dbb9b51c89a8e"));
executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
}
@Test
public void testMultiTechnologyIndels() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand +
" -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
" -o %s" +
" -glm DINDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("8f853cc012d05d341eb55656a7354716"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
// Indel parallelization
//@Test
// todo - test fails because for some reason when including -nt we get "PASS" instead of . in filter fields
public void testIndelParallelization() {
String md5 = "e65e7be8bf736a39d86dbb9b51c89a8e";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm DINDEL -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (single thread)", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm DINDEL -o %s -L 1:10,000,000-10,100,000 -nt 2", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (2 threads)", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation +
"NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -glm DINDEL -o %s -L 1:10,000,000-10,100,000 -nt 4", 1,
Arrays.asList(md5));
executeTest("test indel caller parallelization (4 threads)", spec3);
}
// todo - feature not yet fully working with indels
//@Test
public void testWithIndelAllelesPassedIn() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " --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 -glm DINDEL", 1,
Arrays.asList("e95c545b8ae06f0721f260125cfbe1f0"));
executeTest("test MultiSample Pilot2 indels 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 + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000 -glm DINDEL", 1,
Arrays.asList("6c96d76b9bc3aade0c768d7c657ae210"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec2);
}
}