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After talking with Mauricio and Karthik, updated MD5s and added a note about PairHMM causing test variability.

This commit is contained in:
Khalid Shakir 2014-05-13 23:43:53 +08:00
parent 972a82d386
commit 88d7e23c44
1 changed files with 27 additions and 3 deletions
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30
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -348,17 +348,41 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testQualByDepth() throws IOException {
/*
NOTE: Currently, no HC tests explicitly set their PairHMM implementation, such that outputs may vary depending
on the underlying system. You may run into this test failing due to one of many PairHMM versions activating.
Specifically for this test, the site chr 20:10130722 seems to vary in the HC calculated QUAL and QD. This has
NOTHING to do with a problem in the VariantAnnotator, and is an issue with the way PairHMM is used in tests.
According to Karthik, things to look for in the logs that may help indicate that the failure is NOT something
you changed, but the PairHMM switching on you:
- Using un-vectorized C++ implementation of PairHMM
- Using AVX accelerated implementation of PairHMM
- Using SSE4.1 accelerated implementation of PairHMM
- libVectorLoglessPairHMM unpacked successfully from GATK jar file
- Using vectorized implementation of PairHMM
- (Nothing, which I think means another implementation is being used)
Upon any failures in any HC related tests for now, your best bet is to contact Mauricio to make sure that
everything still looks ok.
TODO: Stabilize the PairHMM from arbitrarily running different versions.
*/
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("b6e8ffdab100b0ea1f8cb89e6e29a9ed"));
final File outputVCF = executeTest("testQualByDepth", spec).getFirst().get(0);
final String baseNoQD = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, CEUTRIO_BAM) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -XA QualByDepth";
final WalkerTestSpec specNoQD = new WalkerTestSpec(baseNoQD, 1, Arrays.asList(""));
final WalkerTestSpec specNoQD = new WalkerTestSpec(baseNoQD, 1, Arrays.asList("23785ea79ac6945d086cbf5613885881"));
specNoQD.disableShadowBCF();
final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0);
final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoQD.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A QualByDepth";
final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("214799b5d1c0809f042c557155ea6e13"));
final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("4ccdbebcfd02be87ae5b4ad94666f011"));
specAnn.disableShadowBCF();
final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0);