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updating HC integration tests.

This commit is contained in:
Ryan Poplin 2012-12-19 10:12:07 -05:00
parent 902ca7ea70
commit 92185dd5f4
2 changed files with 9 additions and 47 deletions
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18
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -21,30 +21,30 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "b8866e674c0f1ea9338f29a7ebe65207");
HCTest(CEUTRIO_BAM, "", "839de31b41d4186e2b12a5601525e894");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "6f371736b36d99913764e8eecd4394a5");
HCTest(NA12878_BAM, "", "2b68faa0e0493d92491d74b8f731963a");
}
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"eef673f79144fab1033c6e286e7c0af3");
"a2d56179cd19a41f8bfb995e225320bb");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 2";
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testHaplotypeCallerComplexVariants: args=" + args, spec);
}
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "883871f8bb4099f69fd804f8a6181954");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd8d2ae8db9d98e932b0a7f345631eec");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -66,20 +66,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "aff11b014ca42bfa301bcced5f5e54dd");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "6380e25c1ec79c6ae2f891ced15bf4e1");
}
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("f9881d61694659b2fdc4c092d20d48b6"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3a096d6139d15dcab82f5b091d08489d"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3f589ef62793ac452bbcc99a77488657"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a518c7436544f2b5f71c9d9427ce1cce"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -93,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("4c5ab9e677a0aed6a430055989e27888"));
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
}

38
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
View File

@ -146,44 +146,6 @@ public class SimpleDeBruijnAssemblerUnitTest extends BaseTest {
Assert.assertTrue(graphEquals(graph, expectedGraph));
}
@Test(enabled=false)
// not ready yet
public void testBasicGraphCreation() {
final ArtificialReadPileupTestProvider refPileupTestProvider = new ArtificialReadPileupTestProvider(1,"ref");
final byte refBase = refPileupTestProvider.getReferenceContext().getBase();
final String altBase = (refBase==(byte)'A'?"C":"A");
final int matches = 50;
final int mismatches = 50;
Map<String,AlignmentContext> refContext = refPileupTestProvider.getAlignmentContextFromAlleles(0, altBase, new int[]{matches, mismatches}, false, 30);
PrintStream graphWriter = null;
try{
graphWriter = new PrintStream("du.txt");
} catch (Exception e) {}
SimpleDeBruijnAssembler assembler = new SimpleDeBruijnAssembler(true,graphWriter);
final Haplotype refHaplotype = new Haplotype(refPileupTestProvider.getReferenceContext().getBases());
refHaplotype.setIsReference(true);
assembler.createDeBruijnGraphs(refContext.get(refPileupTestProvider.getSampleNames().get(0)).getBasePileup().getReads(), refHaplotype);
/* // clean up the graphs by pruning and merging
for( final DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph : graphs ) {
SimpleDeBruijnAssembler.pruneGraph( graph, PRUNE_FACTOR );
//eliminateNonRefPaths( graph );
SimpleDeBruijnAssembler.mergeNodes( graph );
}
*/
if( graphWriter != null ) {
assembler.printGraphs();
}
int k=2;
// find the best paths in the graphs
// return findBestPaths( refHaplotype, fullReferenceWithPadding, refLoc, activeAllelesToGenotype, activeRegion.getExtendedLoc() );
}
@Test(enabled = true)
public void testEliminateNonRefPaths() {
DefaultDirectedGraph<DeBruijnVertex,DeBruijnEdge> graph = new DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge>(DeBruijnEdge.class);