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

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

This commit is contained in:
Joel Thibault 2012-05-01 16:10:38 -04:00
parent aa4d41cce0 51af61b5d7
commit c255dd5917
6 changed files with 88 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -28,7 +28,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
*/
protected static Logger logger = Logger.getLogger(TraversalEngine.class);
private final Queue<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
private final LinkedList<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
@Override
@ -112,7 +112,20 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
final List<ActiveRegion> activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize );
// add active regions to queue of regions to process
workQueue.addAll( activeRegions );
// first check if can merge active regions over shard boundaries
if( !activeRegions.isEmpty() ) {
if( !workQueue.isEmpty() ) {
final ActiveRegion last = workQueue.getLast();
final ActiveRegion first = activeRegions.get(0);
if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= maxRegionSize ) {
workQueue.removeLast();
activeRegions.remove(first);
workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) );
}
}
workQueue.addAll( activeRegions );
}
logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." );
// now go and process all of the active regions

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -376,7 +376,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
}
}
// indel likelihoods are stric log-probs, not phred scored
// indel likelihoods are strict log-probs, not phred scored
double overallScore = 0.0;
for (final double[] readHaplotypeScores : haplotypeScores) {
overallScore += MathUtils.arrayMin(readHaplotypeScores);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -419,7 +419,7 @@ public class UnifiedGenotyperEngine {
// if we are subsetting alleles (either because there were too many or because some were not polymorphic)
// then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
if ( myAlleles.size() != vc.getAlleles().size() )
if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // TODO - this function doesn't work with mixed records or records that started as mixed and then became non-mixed
vcCall = VariantContextUtils.reverseTrimAlleles(vcCall);
if ( annotationEngine != null && !limitedContext && rawContext.hasBasePileup() ) {

72
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -37,6 +37,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.SampleUtils;
@ -243,6 +246,16 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis", required=false)
protected boolean EXCLUDE_FILTERED = false;
/**
* This argument triggers re-genotyping of the selected samples through the Exact calculation model. Note that this is truly the
* mathematically correct way to select samples (especially when calls were generated from low coverage sequencing data); using the
* hard genotypes to select (i.e. the default mode of SelectVariants) can lead to false positives when errors are confused for variants
* in the original genotyping. We decided not to set the --regenotype option as the default though as the output can be unexpected if
* a user is strictly comparing against the original genotypes (GTs) in the file.
*/
@Argument(fullName="regenotype", shortName="regenotype", doc="re-genotype the selected samples based on their GLs (or PLs)", required=false)
protected Boolean REGENOTYPE = false;
private UnifiedGenotyperEngine UG_engine = null;
/**
* When this argument is used, we can choose to include only multiallelic or biallelic sites, depending on how many alleles are listed in the ALT column of a vcf.
@ -440,6 +453,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
SELECT_RANDOM_FRACTION = fractionRandom > 0;
if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");
if ( REGENOTYPE ) {
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
UAC.NO_SLOD = true;
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
}
/** load in the IDs file to a hashset for matching */
if ( rsIDFile != null ) {
@ -519,7 +539,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
continue;
VariantContext sub = subsetRecord(vc, samples, EXCLUDE_NON_VARIANTS);
if ( (sub.isPolymorphicInSamples() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(tracker, ref, context, sub)).filters(sub.getFiltersMaybeNull());
addAnnotations(builder, sub);
sub = builder.make();
}
if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) {
boolean failedJexlMatch = false;
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
if ( !VariantContextUtils.match(sub, jexl) ) {
@ -728,6 +755,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
return recomputedVCs;
}
private boolean hasPLs(final VariantContext vc) {
for ( Genotype g : vc.getGenotypes() ) {
if ( g.hasLikelihoods() )
return true;
}
return false;
}
/**
* Checks if vc has a variant call for (at least one of) the samples.
* @param vc the variant rod VariantContext. Here, the variant is the dataset you're looking for discordances to (e.g. HapMap)
@ -883,9 +918,26 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
builder.genotypes(newGC);
addAnnotations(builder, sub);
return builder.make();
}
private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC) {
if (KEEP_ORIGINAL_CHR_COUNTS) {
if ( originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
builder.attribute("AC_Orig", originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
if ( originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )
builder.attribute("AF_Orig", originalVC.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
if ( originalVC.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) )
builder.attribute("AN_Orig", originalVC.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
}
VariantContextUtils.calculateChromosomeCounts(builder, false);
int depth = 0;
for (String sample : sub.getSampleNames()) {
Genotype g = sub.getGenotype(sample);
for (String sample : originalVC.getSampleNames()) {
Genotype g = originalVC.getGenotype(sample);
if ( g.isNotFiltered() ) {
@ -895,21 +947,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
}
}
}
if (KEEP_ORIGINAL_CHR_COUNTS) {
if ( sub.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
builder.attribute("AC_Orig", sub.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
if ( sub.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )
builder.attribute("AF_Orig", sub.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY));
if ( sub.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) )
builder.attribute("AN_Orig", sub.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
}
VariantContextUtils.calculateChromosomeCounts(builder, false);
builder.attribute("DP", depth);
return builder.make();
}
private void randomlyAddVariant(int rank, VariantContext vc) {

4
public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java
View File

@ -158,7 +158,9 @@ public class ActivityProfile {
// find the best place to break up the large active region
Double minProb = Double.MAX_VALUE;
int cutPoint = -1;
for( int iii = curStart + 50; iii < curEnd - 50; iii++ ) { // BUGBUG: assumes maxRegionSize >> 50
final int size = curEnd - curStart + 1;
for( int iii = curStart + (int)(size*0.25); iii < curEnd - (int)(size*0.25); iii++ ) {
if( isActiveList.get(iii) < minProb ) { minProb = isActiveList.get(iii); cutPoint = iii; }
}
final List<ActiveRegion> leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList<ActiveRegion>());

13
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -116,6 +116,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testUsingDbsnpName--" + testFile, spec);
}
@Test
public void testRegenotype() {
String testFile = validationDataLocation + "combine.3.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("0fd8e52bdcd1f4b921d8fb5c689f196a")
);
executeTest("testRegenotype--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = validationDataLocation + "selectVariants.onePosition.vcf";