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Constant precision for floating point numbers. Added integration test - carries over tests from VariantEval with the necessary modifications to command-line arguments and md5s. Disabled use of 'synchronized' keyword because I clearly don't get how that keyword is supposed to work yet... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5107 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-28 05:19:18 +00:00
parent f29bb0639b
commit 9cb1ae384c
3 changed files with 192 additions and 3 deletions
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15
java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
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@ -546,7 +546,20 @@ public class GATKReportTable {
Object obj = columns.get(columnName).getWithoutSideEffects(primaryKey);
if (needsPadding) { out.printf(" "); }
out.printf(columnWidths.get(columnName), obj == null ? "null" : obj.toString());
String value = "null";
if (obj != null) {
if (obj instanceof Float) {
value = String.format("%.8f", (Float) obj);
} else if (obj instanceof Double) {
value = String.format("%.8f", (Double) obj);
} else {
value = obj.toString();
}
}
//out.printf(columnWidths.get(columnName), obj == null ? "null" : obj.toString());
out.printf(columnWidths.get(columnName), value);
needsPadding = true;
}

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/newvarianteval/util/NewEvaluationContext.java
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@ -52,7 +52,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
synchronized ( evaluation ) {
//synchronized ( evaluation ) {
// we always call update0 in case the evaluation tracks things like number of bases covered
//evaluation.update0(tracker, ref, context);
@ -77,7 +77,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
default:
throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
}
}
//}
}
}

176
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/NewVariantEvalIntegrationTest.java 100755
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@ -0,0 +1,176 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class NewVariantEvalIntegrationTest extends WalkerTest {
private static String cmdRoot = "-T NewVariantEval" +
" -R " + b36KGReference;
private static String root = cmdRoot +
" -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -B:eval,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes,VCF " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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";
private static String[] testsEnumerations = {root, rootGZ};
@Test
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -o %s",
1, Arrays.asList("8ddc1c4a86cb3f4c22346497785b23e3"));
//executeTestParallel("testSelect1", spec);
executeTest("testSelect1", spec);
}
}
// @Test
// public void testSelect2() {
// String extraArgs = "-L 1:1-10,000,000";
// WalkerTestSpec spec = new WalkerTestSpec( withSelect(withSelect(root, "DP < 50", "DP50"), "set==\"Intersection\"", "intersection") + " " + extraArgs + " -o %s",
// 1, Arrays.asList(""));
// //executeTestParallel("testSelect2", spec);
// executeTest("testSelect2", spec);
// }
@Test
public void testVEGenotypeConcordance() {
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 -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("7a6754176b573d14b6be7c808a04929d"));
//executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
executeTest("testVEGenotypeConcordance" + vcfFile, spec);
}
}
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "ffd1abed44faf1590d9026e478b2f8ee");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "32c2411fbf58bae5750c8229d15b98eb");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
String md5 = entry.getValue();
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec( tests + " " + extraArgs + " -o %s",
1, // just one output file
Arrays.asList(md5));
//executeTestParallel("testVESimple", spec);
executeTest("testVESimple", spec);
}
}
}
@Test
public void testVEComplex() {
HashMap<String, String> expectations = new HashMap<String, String>();
String extraArgs1 = "-L " + validationDataLocation + "chr1_b36_pilot3.interval_list -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator" +
" -B:dbsnp_130,dbSNP " + GATKDataLocation + "dbsnp_130_b36.rod" +
" -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
String matchingMD5 = "6c2fa6573cc57ef8795e9cce2b654d0b";
expectations.put("", matchingMD5);
expectations.put(" -knownName comp_hapmap -knownName dbsnp", matchingMD5);
expectations.put(" -knownName comp_hapmap", "6c2fa6573cc57ef8795e9cce2b654d0b");
for (String tests : testsEnumerations) {
for (Map.Entry<String, String> entry : expectations.entrySet()) {
String extraArgs2 = entry.getKey();
String md5 = entry.getValue();
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs1 + extraArgs2 + " -o %s",
1, // just one output file
Arrays.asList(md5));
//executeTestParallel("testVEComplex", spec);
executeTest("testVEComplex", spec);
}
}
}
// @Test
// public void testVEGenomicallyAnnotated() {
// String vecmd = "-T NewVariantEval" +
// " -R " + b36KGReference +
// " -L 21" +
// " -D " + GATKDataLocation + "dbsnp_129_b36.rod" +
// " -EV CountFunctionalClasses -noEV" +
// " -B:eval,VCF " + validationDataLocation + "test.filtered.maf_annotated.vcf" +
// " -o %s";
// String md5 = "";
//
// WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5));
// executeTestParallel("testVEGenomicallyAnnotated", spec);
// //executeTest("testVEGenomicallyAnnotated", spec);
// }
//
// @Test
// public void testVEWriteVCF() {
// String extraArgs = "-L 1:1-10,000,000 -NO_HEADER -family NA19238+NA19239=NA19240 -mvq 30 -EV MendelianViolationEvaluator";
// for (String tests : testsEnumerations) {
// WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s -NO_HEADER",
// 2,
// Arrays.asList("50321436a65ef7d574286cb0a1c55f7e", "d4bdd06ed5cb1aff1dfee8b69d5d17b8"));
// executeTestParallel("testVEWriteVCF", spec);
// //executeTest("testVEWriteVCF", spec);
// }
// }
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T NewVariantEval -R "+b36KGReference+" -o %s -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("929e4ec46fb6957c29803531322bb35e"));
//executeTestParallel("testACDiscordanceAtAC1EvalAC2Comp",spec);
executeTest("testCompVsEvalAC",spec);
}
private static String withSelect(String cmd, String select, String name) {
return String.format("%s -select '%s' -selectName %s", cmd, select, name);
}
@Test
public void testTranches() {
String extraArgs = "-T NewVariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("68044a69f03ba4cc11d2061cc96e9eb5"));
//executeTestParallel("testTranches",spec);
executeTest("testTranches",spec);
}
// @Test
// public void testVEValidatePass() {
// String extraArgs = "-L 1:1-10,000,000";
// for (String tests : testsEnumerations) {
// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 4.0) + " " + extraArgs + " -o %s",
// 1, Arrays.asList("8a0203f0533b628ad7f1f230a43f105f"));
// executeTestParallel("testVEValidatePass", spec);
// }
// }
//
// @Test
// public void testVEValidateFail() {
// String extraArgs = "-L 1:1-10,000,000";
// for (String tests : testsEnumerations) {
// WalkerTestSpec spec = new WalkerTestSpec(withValidateTiTv(withSelect(tests, "DP < 50", "DP50"), 1.0, 1.2) + " " + extraArgs + " -o %s",
// 1, UserException.class);
// executeTestParallel("testVEValidateFail", spec);
// }
// }
//
// private static String withValidateTiTv(String cmd, double min, double max) {
// return String.format("%s -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio >= %2$s' -validate 'eval.comp_genotypes.all.called.all.titv.tiTvRatio <= %3$s'", cmd, min, max);
// }
}