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updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version 

to the vlidation directory), using the same md5sum.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-06-09 01:47:04 +00:00
parent 2b31975cb4
commit 6d5556939d
4 changed files with 41 additions and 25 deletions
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60
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -17,13 +17,21 @@ public class
" -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf -reportType Grep";
private static String rootGZ = cmdRoot +
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B eval,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
" -B comp_genotypes,VCF," + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz -reportType Grep";
private static String[] testsEnumerations = {root, rootGZ};
@Test
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
WalkerTestSpec spec = new WalkerTestSpec( withSelect(root, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
1, Arrays.asList("5a330d359b5c7ea0dfa6698b4830db82"));
executeTest("testSelect1", spec);
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
1, Arrays.asList("5a330d359b5c7ea0dfa6698b4830db82"));
executeTest("testSelect1", spec);
}
}
@Test
@ -36,10 +44,14 @@ public class
@Test
public void testVEGenotypeConcordance() {
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B eval,VCF," + validationDataLocation + "GenotypeConcordanceEval.vcf -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
1, // just one output file
Arrays.asList("608b32189818df7271c546dd5f257033"));
executeTest("testVEGenotypeConcordance", spec);
String vcfFiles[] = {"GenotypeConcordanceEval.vcf", "GenotypeConcordanceEval.vcf.gz"};
for (String vcfFile : vcfFiles) {
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -B eval,VCF," + validationDataLocation + vcfFile + " -B comp,VCF," + validationDataLocation + "GenotypeConcordanceComp.vcf -E GenotypeConcordance -reportType CSV -o %s",
1,
Arrays.asList("608b32189818df7271c546dd5f257033"));
executeTest("testVEGenotypeConcordance" + vcfFile, spec);
}
}
@Test
@ -51,11 +63,12 @@ public class
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
String md5 = entry.getValue();
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s",
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testVESimple", spec);
executeTest("testVESimple", spec);
}
}
}
@ -71,25 +84,28 @@ public class
expectations.put("", matchingMD5);
expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
expectations.put(" -known comp_hapmap", "fd9cd9970f7e509ca476502869063929");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
String md5 = entry.getValue();
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs2 = entry.getKey();
String md5 = entry.getValue();
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs1 + extraArgs2 + " -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testVEComplex", spec);
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
1, // just one output file
Arrays.asList(md5));
executeTest("testVEComplex", spec);
}
}
}
@Test
public void testVEWriteVCF() {
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
2,
Arrays.asList("521837758da151b84fca57fd1bb7dad1", "b4a42c90318adc88361691ece50426f2"));
executeTest("testVEWriteVCF", spec);
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
2,
Arrays.asList("521837758da151b84fca57fd1bb7dad1", "b4a42c90318adc88361691ece50426f2"));
executeTest("testVEWriteVCF", spec);
}
}
private static String withSelect(String cmd, String select, String name) {

3
settings/repository/org.broad/tribble-88.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="88" status="integration" publication="20100603124200" />
</ivy-module>

BIN
settings/repository/org.broad/tribble-88.jar → settings/repository/org.broad/tribble-98.jar
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3
settings/repository/org.broad/tribble-98.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="98" status="integration" publication="20100608124200" />
</ivy-module>