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When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5272 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-18 06:26:38 +00:00
parent 1bc5c7e99b
commit 9ddee96f93
4 changed files with 56 additions and 31 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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@ -75,7 +75,7 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
} }
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
boolean evalIsGood = eval != null; boolean evalIsGood = eval != null && eval.isVariant();
boolean expectingIndels = eval != null && eval.isIndel(); boolean expectingIndels = eval != null && eval.isIndel();
boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ; boolean compIsGood = expectingIndels ? comp != null && comp.isNotFiltered() && comp.isIndel() : comp != null && comp.isNotFiltered() && comp.isSNP() ;

2
java/test/org/broadinstitute/sting/WalkerTest.java
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@ -71,7 +71,7 @@ public class WalkerTest extends BaseTest {
return md5s; return md5s;
} }
public String cmdLineBuilder(String ... arguments) { public String buildCommandLine(String... arguments) {
String cmdline = ""; String cmdline = "";
for ( int argIndex = 0; argIndex < arguments.length; argIndex++ ) { for ( int argIndex = 0; argIndex < arguments.length; argIndex++ ) {

4
java/test/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotatorIntegrationTest.java
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@ -48,7 +48,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
@Test @Test
public void testGenomicAnnotatorOnIndels() { public void testGenomicAnnotatorOnIndels() {
WalkerTestSpec testOnIndels = new WalkerTestSpec( WalkerTestSpec testOnIndels = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T GenomicAnnotator", "-T GenomicAnnotator",
"-R " + b37KGReference, "-R " + b37KGReference,
"-L 22:10000000-20000000", "-L 22:10000000-20000000",
@ -65,7 +65,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
@Test @Test
public void testGenomicAnnotatorOnSNPsAndIndels() { public void testGenomicAnnotatorOnSNPsAndIndels() {
WalkerTestSpec testOnSNPsAndIndels = new WalkerTestSpec( WalkerTestSpec testOnSNPsAndIndels = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T GenomicAnnotator", "-T GenomicAnnotator",
"-R " + b37KGReference, "-R " + b37KGReference,
"-L 22:10000000-20000000", "-L 22:10000000-20000000",

79
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval; package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.Arrays; import java.util.Arrays;
@ -11,6 +10,8 @@ import java.util.Map;
public class VariantEvalIntegrationTest extends WalkerTest { public class VariantEvalIntegrationTest extends WalkerTest {
private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval"; private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf"; private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
private static String cmdRoot = "-T VariantEval" + private static String cmdRoot = "-T VariantEval" +
" -R " + b36KGReference; " -R " + b36KGReference;
@ -27,22 +28,6 @@ public class VariantEvalIntegrationTest extends WalkerTest {
private static String[] testsEnumerations = {root, rootGZ}; private static String[] testsEnumerations = {root, rootGZ};
/*
private String cmdLineBuilder(String ... arguments) {
String cmdline = "";
for ( int argIndex = 0; argIndex < arguments.length; argIndex++ ) {
cmdline += arguments[argIndex];
if (argIndex < arguments.length - 1) {
cmdline += " ";
}
}
return cmdline;
}
*/
@Test @Test
public void testFundamentalsCountVariantsSNPsAndIndels() { public void testFundamentalsCountVariantsSNPsAndIndels() {
// nProcessedLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38 // nProcessedLoci = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | awk '{ print length($4) }' | ~kiran/bin/SimpleStats = 38
@ -59,7 +44,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -91,7 +76,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVarKnown = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5 // nHomVarKnown = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | grep DBSNP129 | awk '{ if ($5 != ".") print $0 }' | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -124,7 +109,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVarFail = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 3 // nHomVarFail = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep -v PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 3
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -158,7 +143,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep NONCPG | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -179,7 +164,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test @Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() { public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -200,7 +185,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test @Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() { public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -230,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "1/1") print $0 }' | wc -l = 2 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ if ($10 ~ "1/1") print $0 }' | wc -l = 2
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -259,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5
// nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4 // nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -290,7 +275,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '1/1' = 5
// nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4 // nNoCalls = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk -F"[\t;]" '{ for (i = 1; i < NF; i++) if ($i ~ "DP=") print $i, $0 }' | sed 's/^DP=//' | awk '{ if ($1 < 20) print $11 "\n" $12 "\n" $13 }' | grep -c '\.\/\.' = 4
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-D " + b37dbSNP129, "-D " + b37dbSNP129,
@ -328,7 +313,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
// nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5 // nHomVar = grep -v '#' FundamentalsTest.annotated.db.subset.snps_and_indels.vcf | grep PASS | awk '{ for (i = 10; i <= 12; i++) if ($i ~ "1/1") print $0 }' | wc -l = 5
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
cmdLineBuilder( buildCommandLine(
"-T VariantEval", "-T VariantEval",
"-R " + b37KGReference, "-R " + b37KGReference,
"-B:eval,VCF " + fundamentalTestVCF, "-B:eval,VCF " + fundamentalTestVCF,
@ -494,6 +479,46 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTestParallel("testMultipleCompTracks",spec); executeTestParallel("testMultipleCompTracks",spec);
} }
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
String md5 = "454a1750fd36525f24172b21af5f49de";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-D " + b37dbSNP129,
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList(md5)
);
executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-subset", spec);
WalkerTestSpec spec2 = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-D " + b37dbSNP129,
"-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
"-noEV",
"-EV CompOverlap",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList(md5)
);
executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-onesample", spec2);
}
// @Test // @Test
// public void testVEGenomicallyAnnotated() { // public void testVEGenomicallyAnnotated() {
// String vecmd = "-T VariantEval" + // String vecmd = "-T VariantEval" +