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Reduce intervals of integration tests in HaplotypeCallerIntegrationTest class 

Story:

   https://www.pivotaltracker.com/story/show/74858854

Changes:

    Intervals have been shrunk so that the test run in 15s or less.
This commit is contained in:
Valentin Ruano-Rubio 2014-08-15 11:29:53 -04:00
parent 20f72e1d0c
commit 2f79042dee
1 changed files with 17 additions and 14 deletions
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31
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -75,6 +75,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final static String NA12878_PCRFREE250_ADAPTER_TRIMMED = privateTestDir + "PCRFree.2x250.b37_decoy.NA12878.adapter_trimmed-10000000-11000000.bam";
final static String CEUTRIO_MT_TEST_BAM = privateTestDir + "CEUTrio.HiSeq.b37.MT.1_50.bam";
final static String INTERVALS_FILE = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals";
final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
private void HCTest(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
@ -114,8 +115,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"4047ea70f37b59b782402f678ea2dfee");
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
"669aac2aa9c22881eda86ee53b13351a");
}
@Test
@ -226,25 +228,25 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestDBSNPAnnotationWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("3d1fcf8b4a1d8d328c0a0aae5f4558eb"));
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("89b83443b0092530bdad595b14f67f2d"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@Test
public void HCTestDBSNPAnnotationWEx() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
"-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+ " -L " + hg19Intervals + " -isr INTERSECTION", 1,
Arrays.asList("e64e06ae90a8eab52cabe3687992da73"));
Arrays.asList("76277d8ea79e2901364a26740d2f50ae"));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
}
@Test
public void HCTestDBSNPAnnotationWGSGraphBased() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("7748a90ffd7daa15a8d518fc528bfcc5"));
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
Arrays.asList("9aa0a5946de59884c46cde74f817e77d"));
executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
}
@ -260,7 +262,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestGraphBasedPCRFreePositiveLogLkFix() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,000,000-11,000,000 "
"-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
, 1,
Arrays.asList(""));
executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
@ -275,16 +277,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestAggressivePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
Arrays.asList("a97154c320a04f3e21f23b8c793d4111"));
"-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("9b8a822e5ead66f09227d82c94315e59"));
executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
}
@Test
public void HCTestConservativePcrIndelModelWGS() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
Arrays.asList("df871f2b5cbb01bdc758614ef1923bf7"));
"-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
Arrays.asList("1d24772716916eede70f6c157d46e931"));
executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
}
@ -299,12 +301,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("testGraphBasedNoSuchEdgeBugFix", spec);
}
// This test takes longer than 15 secs ... ~ 25-35 ,
@Test
public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list",
HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("f2deea31d32c0cfe3298755a83171c8f"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("90ab538102f5faf4f4a07860cb8fa1b1"));
spec.disableShadowBCF();
executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
}