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Merged bug fix from Stable into Unstable

This commit is contained in:
Ryan Poplin 2012-08-03 10:45:01 -04:00
parent 51bd03cc36 f40d0a0a28
commit 8817fc70d1
4 changed files with 34 additions and 13 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -196,7 +196,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
for( final VariantContext vc : VCs ) {
if( VariantRecalibrator.checkRecalibrationMode( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
if( VariantDataManager.checkVariationClass( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
final VariantContext recalDatum = getMatchingRecalVC(vc, recals);
if( recalDatum == null ) {

31
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -273,11 +274,37 @@ public class VariantDataManager {
}
private boolean isValidVariant( final VariantContext evalVC, final VariantContext trainVC, final boolean TRUST_ALL_POLYMORPHIC) {
return trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() &&
((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) &&
return trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && checkVariationClass( evalVC, trainVC ) &&
(TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphicInSamples());
}
protected static boolean checkVariationClass( final VariantContext evalVC, final VariantContext trainVC ) {
switch( trainVC.getType() ) {
case SNP:
case MNP:
return checkVariationClass( evalVC, VariantRecalibratorArgumentCollection.Mode.SNP );
case INDEL:
case MIXED:
case SYMBOLIC:
return checkVariationClass( evalVC, VariantRecalibratorArgumentCollection.Mode.INDEL );
default:
return false;
}
}
protected static boolean checkVariationClass( final VariantContext evalVC, final VariantRecalibratorArgumentCollection.Mode mode ) {
switch( mode ) {
case SNP:
return evalVC.isSNP() || evalVC.isMNP();
case INDEL:
return evalVC.isIndel() || evalVC.isMixed() || evalVC.isSymbolic();
case BOTH:
return true;
default:
throw new ReviewedStingException( "Encountered unknown recal mode: " + mode );
}
}
public void writeOutRecalibrationTable( final VariantContextWriter recalWriter ) {
// we need to sort in coordinate order in order to produce a valid VCF
Collections.sort( data, new Comparator<VariantDatum>() {

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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@ -245,7 +245,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
for( final VariantContext vc : tracker.getValues(input, context.getLocation()) ) {
if( vc != null && ( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) {
if( checkRecalibrationMode( vc, VRAC.MODE ) ) {
if( VariantDataManager.checkVariationClass( vc, VRAC.MODE ) ) {
final VariantDatum datum = new VariantDatum();
// Populate the datum with lots of fields from the VariantContext, unfortunately the VC is too big so we just pull in only the things we absolutely need.
@ -268,12 +268,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
return mapList;
}
public static boolean checkRecalibrationMode( final VariantContext vc, final VariantRecalibratorArgumentCollection.Mode mode ) {
return mode == VariantRecalibratorArgumentCollection.Mode.BOTH ||
(mode == VariantRecalibratorArgumentCollection.Mode.SNP && vc.isSNP()) ||
(mode == VariantRecalibratorArgumentCollection.Mode.INDEL && (vc.isIndel() || vc.isMixed()));
}
//---------------------------------------------------------------------------------------------------------------
//
// reduce

6
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -26,9 +26,9 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
}
VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
"62f81e7d2082fbc71cae0101c27fefad", // tranches
"b9709e4180e56abc691b208bd3e8626c", // recal file
"75c178345f70ca2eb90205662fbdf968"); // cut VCF
"f360ce3eb2b0b887301be917a9843e2b", // tranches
"287fea5ea066bf3fdd71f5ce9b58eab3", // recal file
"356b9570817b9389da71fbe991d8b2f5"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {