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Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-08-15 13:32:07 -04:00
parent 7599f94296 87e41c83c5
commit db92671b7f
6 changed files with 70 additions and 14 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -57,8 +57,6 @@ public class GATKArgumentCollection {
public GATKArgumentCollection() {
}
public Map<String, String> walkerArgs = new HashMap<String, String>();
// parameters and their defaults
@Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
public List<String> samFiles = new ArrayList<String>();

10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -646,15 +646,17 @@ public class UnifiedGenotyperEngine {
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null ) {
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
return models;
}
if ( vcInput.isSNP() ) {
// ignore SNPs if the user chose INDEL mode only
if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") )
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
}
}
else if ( vcInput.isIndel() || vcInput.isMixed() ) {
// ignore INDELs if the user chose SNP mode only
if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") )
@ -759,7 +761,7 @@ public class UnifiedGenotyperEngine {
public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {
if ( tracker == null || ref == null || logger == null )
throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
return null;
VariantContext vc = null;
// search for usable record

4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
View File

@ -51,6 +51,10 @@ public class AlleleCount extends VariantStratifier {
AC = Math.max(AC, eval.getCalledChrCount(allele));
}
// make sure that the AC isn't invalid
if ( AC > eval.getCalledChrCount() )
throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount()));
return Collections.singletonList((Object) AC);
} else {
return Collections.emptyList();

19
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -470,6 +470,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
UAC.NO_SLOD = true;
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
@ -567,7 +568,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(tracker, ref, context, sub)).filters(sub.getFiltersMaybeNull());
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
}
@ -730,7 +731,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if ( vc.getAlleles().size() != sub.getAlleles().size() )
newGC = VariantContextUtils.stripPLs(sub.getGenotypes());
//Remove a fraction of the genotypes if needed
// if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
if ( vc.getNSamples() != sub.getNSamples() ) {
builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY);
builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
}
// Remove a fraction of the genotypes if needed
if ( fractionGenotypes > 0 ){
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
for ( Genotype genotype : newGC ) {
@ -767,17 +774,21 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContextUtils.calculateChromosomeCounts(builder, false);
boolean sawDP = false;
int depth = 0;
for (String sample : originalVC.getSampleNames()) {
Genotype g = originalVC.getGenotype(sample);
if ( ! g.isFiltered() ) {
if ( g.hasDP() )
if ( g.hasDP() ) {
depth += g.getDP();
sawDP = true;
}
}
}
builder.attribute("DP", depth);
if ( sawDP )
builder.attribute("DP", depth);
}
private void randomlyAddVariant(int rank, VariantContext vc) {

15
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -585,6 +585,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
executeTest("testStandardIndelEval", spec);
}
@Test
public void testBadACValue() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-eval " + privateTestDir + "vcfexample.withBadAC.vcf",
"-noST -ST AlleleCount",
"-noEV -EV VariantSummary"
),
0,
UserException.class);
executeTest("testBadACValue", spec);
}
@Test()
public void testIncompatibleEvalAndStrat() {

34
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -34,7 +34,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn B -sn C --variant " + testfile),
1,
Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6")
Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57")
);
executeTest("testRepeatedLineSelection--" + testfile, spec);
@ -49,7 +49,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
+ b37hapmapGenotypes + " -disc " + testFile
+ " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
1,
Arrays.asList("54289033d35d32b8ebbb38c51fbb614c")
Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf")
);
spec.disableShadowBCF();
@ -135,7 +135,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("d12ae1617deb38f5ed712dc326935b9a")
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
);
executeTest("testUsingDbsnpName--" + testFile, spec);
@ -148,12 +148,38 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("c22ad8864d9951403672a24c20d6c3c2")
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
);
executeTest("testRegenotype--" + testFile, spec);
}
@Test
public void testRemoveMLE() {
String testFile = privateTestDir + "vcfexample.withMLE.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
);
executeTest("testRemoveMLE--" + testFile, spec);
}
@Test
public void testRemoveMLEAndRegenotype() {
String testFile = privateTestDir + "vcfexample.withMLE.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
);
executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = privateTestDir + "selectVariants.onePosition.vcf";