zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-02 22:33:50 +00:00
parent cf15819db5
commit cb6454bf98
13 changed files with 60 additions and 23 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -83,6 +83,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
protected Boolean NO_STANDARD_MODULES = false;
// Other arguments
@Argument(fullName="numSamples", shortName="ns", doc="Number of samples (used if no samples are available in the VCF file", required=false)
protected Integer NUM_SAMPLES = 0;
@Argument(fullName="minPhaseQuality", shortName="mpq", doc="Minimum phasing quality", required=false)
protected double MIN_PHASE_QUALITY = 10.0;
@ -376,7 +379,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
// Load the sample list
sampleNamesForEvaluation.addAll(SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
numSamples = sampleNamesForEvaluation.size();
numSamples = NUM_SAMPLES > 0 ? NUM_SAMPLES : sampleNamesForEvaluation.size();
if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
sampleNamesForStratification.addAll(sampleNamesForEvaluation);
@ -507,7 +510,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
if ( vc != null ) {
VariantContext vcsub = vc;
if (vc.hasGenotypes(sampleNamesForEvaluation)) {
if (vc.hasGenotypes() && vc.hasGenotypes(sampleNamesForEvaluation)) {
vcsub = getSubsetOfVariantContext(vc, sampleNamesForEvaluation);
}
@ -516,7 +519,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
}
// Now, if stratifying, split the subsetted vc per sample and add each as a new context
if ( trackPerSample ) {
if ( vc.hasGenotypes() && trackPerSample ) {
for ( String sampleName : sampleNamesForEvaluation ) {
VariantContext samplevc = getSubsetOfVariantContext(vc, sampleName);
@ -669,7 +672,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
HashMap<VariantStratifier, ArrayList<String>> stateMap = new HashMap<VariantStratifier, ArrayList<String>>();
for ( VariantStratifier vs : stratificationObjects ) {
ArrayList<String> states = vs.getRelevantStates(ref, comp, compName, eval, sampleName);
ArrayList<String> states = vs.getRelevantStates(ref, comp, compName, eval, evalName, sampleName);
stateMap.put(vs, states);
}

16
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/SimpleMetricsByAC.java
View File

@ -123,8 +123,9 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
ac = Integer.valueOf(eval.getAttributeAsString("AC"));
}
if ( ac != -1 )
if ( ac != -1 ) {
metrics.get(ac).update(eval);
}
}
}
@ -150,19 +151,22 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
}
public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (numSamples == 0) {
return null;
}
final String interesting = null;
if (eval != null ) {
if (eval != null) {
if ( metrics == null ) {
int nSamples = numSamples;
if ( nSamples != -1 )
if ( nSamples != -1 ) {
metrics = new MetricsByAc(2 * nSamples);
}
}
if ( eval.isSNP() &&
eval.isBiallelic() &&
metrics != null ) {
if ( eval.isSNP() && eval.isBiallelic() && metrics != null ) {
metrics.incrValue(eval);
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
View File

@ -24,7 +24,7 @@ public class CompRod extends VariantStratifier implements RequiredStratification
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add(compName);

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
View File

@ -22,7 +22,7 @@ public class CpG extends VariantStratifier implements StandardStratification {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
boolean isCpG = false;
if (ref != null && ref.getBases() != null) {
String fwRefBases = new String(ref.getBases());

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
View File

@ -52,7 +52,7 @@ public class Degeneracy extends VariantStratifier {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("all");

6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
View File

@ -17,17 +17,17 @@ public class EvalRod extends VariantStratifier implements RequiredStratification
this.evalNames = evalNames;
states = new ArrayList<String>();
states.add("eval");
states.addAll(evalNames);
}
public ArrayList<String> getAllStates() {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("eval");
relevantStates.add(evalName);
return relevantStates;
}

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
View File

@ -23,7 +23,7 @@ public class Filter extends VariantStratifier {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("raw");

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
View File

@ -24,7 +24,7 @@ public class FunctionalClass extends VariantStratifier {
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("all");

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
View File

@ -27,7 +27,7 @@ public class JexlExpression extends VariantStratifier implements StandardStratif
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("none");

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
View File

@ -26,7 +26,7 @@ public class Novelty extends VariantStratifier implements StandardStratification
return states;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add("all");

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
View File

@ -22,7 +22,7 @@ public class Sample extends VariantStratifier {
return samples;
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
ArrayList<String> relevantStates = new ArrayList<String>();
relevantStates.add(sampleName);

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
View File

@ -15,7 +15,7 @@ public abstract class VariantStratifier implements Comparable {
return new ArrayList<String>();
}
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
return null;
}

32
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -133,7 +133,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -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("113228ffa35e0f67b8e067860c04171f"));
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d8d59ec86ec9e00abad4ec44741de22f"));
executeTestParallel("testCompVsEvalAC",spec);
//executeTest("testCompVsEvalAC",spec);
}
@ -158,6 +158,36 @@ public class VariantEvalIntegrationTest extends WalkerTest {
//executeTest("testCompOverlap",spec);
}
@Test
public void testEvalTrackWithoutGenotypes() {
String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
" -D " + dbsnp +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2e2c24b49f699506b967befbde5a6fa8"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@Test
public void testMultipleEvalTracksWithoutGenotypes() {
String dbsnp = GATKDataLocation + "dbsnp_129_b37.rod";
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
" -D " + dbsnp +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("144053b8bef5a79b23d0abd17b561294"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
// @Test
// public void testVEValidatePass() {
// String extraArgs = "-L 1:1-10,000,000";