First attempt at removing all traces of extended events from UG; integration tests are expected to fail.
This commit is contained in:
Eric Banks
parent
e61e162c81
commit
e4469a83ee
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@ -32,9 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.clipping.ReadClipper;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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@ -100,43 +98,32 @@ public class ConsensusAlleleCounter {
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int insCount = 0, delCount = 0;
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// quick check of total number of indels in pileup
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for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
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AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
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for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {
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final AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
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if (context.hasExtendedEventPileup()) {
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final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
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insCount += indelPileup.getNumberOfInsertions();
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delCount += indelPileup.getNumberOfDeletions();
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}
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else {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup indelPileup = context.getBasePileup();
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insCount += indelPileup.getNumberOfInsertionsAfterThisElement();
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delCount += indelPileup.getNumberOfDeletionsAfterThisElement();
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}
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}
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if (insCount < minIndelCountForGenotyping && delCount < minIndelCountForGenotyping)
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if ( insCount < minIndelCountForGenotyping && delCount < minIndelCountForGenotyping )
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return Collections.emptyMap();
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for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
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// todo -- warning, can be duplicating expensive partition here
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AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
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final ReadBackedPileup indelPileup;
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if ( !context.hasBasePileup() )
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continue;
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final int nIndelReads, nReadsOverall;
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final ReadBackedPileup indelPileup = context.getBasePileup();
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if (context.hasExtendedEventPileup()) {
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indelPileup = context.getExtendedEventPileup();
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nIndelReads = ((ReadBackedExtendedEventPileup)indelPileup).getNumberOfInsertions() + indelPileup.getNumberOfDeletions();
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nReadsOverall = indelPileup.getNumberOfElements();
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}
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else {
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indelPileup = context.getBasePileup();
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nIndelReads = indelPileup.getNumberOfInsertionsAfterThisElement() + indelPileup.getNumberOfDeletionsAfterThisElement();
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nReadsOverall = indelPileup.getNumberOfElements();
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}
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if ( nIndelReads == 0 || (nIndelReads / (1.0 * nReadsOverall)) < minFractionInOneSample) {
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final int nIndelReads = indelPileup.getNumberOfInsertionsAfterThisElement() + indelPileup.getNumberOfDeletionsAfterThisElement();
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final int nReadsOverall = indelPileup.getNumberOfElements();
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if ( nIndelReads == 0 || (nIndelReads / (1.0 * nReadsOverall)) < minFractionInOneSample ) {
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// if ( nIndelReads > 0 )
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// logger.info("Skipping sample " + sample.getKey() + " with nIndelReads " + nIndelReads + " nReads " + nReadsOverall);
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continue;
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@ -161,7 +148,7 @@ public class ConsensusAlleleCounter {
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*/
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String indelString = p.getEventBases();
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if (isInsertion(p)) {
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if ( p.isBeforeInsertion() ) {
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boolean foundKey = false;
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// copy of hashmap into temp arrayList
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ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>();
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@ -229,7 +216,7 @@ public class ConsensusAlleleCounter {
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}
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}
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else if (isDeletion(p)) {
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else if ( p.isBeforeDeletion() ) {
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indelString = String.format("D%d",p.getEventLength());
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int cnt = consensusIndelStrings.containsKey(indelString)? consensusIndelStrings.get(indelString):0;
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consensusIndelStrings.put(indelString,cnt+1);
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@ -241,25 +228,6 @@ public class ConsensusAlleleCounter {
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return consensusIndelStrings;
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}
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// todo - helper routines to check for extended pileup elements, to remove when extended events are removed
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private static final boolean isInsertion(final PileupElement p) {
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if (p instanceof ExtendedEventPileupElement)
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return ((ExtendedEventPileupElement) p).isInsertion();
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else
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return p.isBeforeInsertion();
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}
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private static boolean isDeletion(final PileupElement p) {
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if (p instanceof ExtendedEventPileupElement)
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return p.isDeletion();
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else
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return p.isBeforeDeletion();
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}
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private List<Allele> consensusCountsToAlleles(final ReferenceContext ref,
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final Map<String, Integer> consensusIndelStrings) {
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final GenomeLoc loc = ref.getLocus();
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@ -120,7 +120,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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if ( sample.hasLikelihoods() ) {
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double[] gls = sample.getLikelihoods().getAsVector();
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if ( MathUtils.sum(gls) < VariantContextUtils.SUM_GL_THRESH_NOCALL )
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if ( MathUtils.sum(gls) < UnifiedGenotyperEngine.SUM_GL_THRESH_NOCALL )
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genotypeLikelihoods.add(gls);
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}
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}
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@ -114,7 +114,7 @@ import java.util.*;
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@Reference(window=@Window(start=-200,stop=200))
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@By(DataSource.REFERENCE)
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@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
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public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker {
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public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker {
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@ArgumentCollection
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private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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@ -173,12 +173,6 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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@Override
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public boolean includeReadsWithDeletionAtLoci() { return true; }
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// enable extended events for indels
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@Override
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public boolean generateExtendedEvents() {
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return (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.SNP && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES);
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}
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/**
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* Inner class for collecting output statistics from the UG
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*/
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@ -281,7 +275,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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* @param rawContext contextual information around the locus
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* @return the VariantCallContext object
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*/
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public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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public List<VariantCallContext> map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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return UG_engine.calculateLikelihoodsAndGenotypes(tracker, refContext, rawContext);
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}
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@ -295,32 +289,40 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
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return lhs;
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}
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public UGStatistics reduce(VariantCallContext value, UGStatistics sum) {
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public UGStatistics reduce(List<VariantCallContext> calls, UGStatistics sum) {
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// we get a point for reaching reduce
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sum.nBasesVisited++;
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// can't call the locus because of no coverage
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if ( value == null )
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return sum;
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boolean wasCallable = false;
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boolean wasConfidentlyCalled = false;
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// A call was attempted -- the base was potentially callable
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sum.nBasesCallable++;
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for ( VariantCallContext call : calls ) {
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if ( call == null )
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continue;
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// the base was confidently callable
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sum.nBasesCalledConfidently += value.confidentlyCalled ? 1 : 0;
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// A call was attempted -- the base was callable
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wasCallable = true;
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// can't make a call here
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if ( !value.shouldEmit )
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return sum;
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// was the base confidently callable?
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wasConfidentlyCalled = call.confidentlyCalled;
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try {
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// we are actually making a call
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sum.nCallsMade++;
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writer.add(value);
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage());
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if ( call.shouldEmit ) {
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try {
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// we are actually making a call
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sum.nCallsMade++;
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writer.add(call);
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage());
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}
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}
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}
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if ( wasCallable )
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sum.nBasesCallable++;
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if ( wasConfidentlyCalled )
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sum.nBasesCalledConfidently++;
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return sum;
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}
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@ -41,7 +41,6 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.variantcontext.*;
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@ -107,6 +106,7 @@ public class UnifiedGenotyperEngine {
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private final GenomeLocParser genomeLocParser;
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private final boolean BAQEnabledOnCMDLine;
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protected static final double SUM_GL_THRESH_NOCALL = VariantContextUtils.SUM_GL_THRESH_NOCALL;
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// ---------------------------------------------------------------------------------------------------------
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//
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@ -150,22 +150,28 @@ public class UnifiedGenotyperEngine {
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* @param rawContext contextual information around the locus
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* @return the VariantCallContext object
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*/
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public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel(tracker, refContext, rawContext );
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if( model == null ) {
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return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null);
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public List<VariantCallContext> calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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final List<VariantCallContext> results = new ArrayList<VariantCallContext>(2);
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final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
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if ( models.isEmpty() ) {
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results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null);
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}
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else {
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for ( final GenotypeLikelihoodsCalculationModel.Model model : models ) {
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final Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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if ( stratifiedContexts == null ) {
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results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null);
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}
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else {
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final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
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if ( vc != null )
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results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model));
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}
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}
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}
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Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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if ( stratifiedContexts == null ) {
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return (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null);
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}
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VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
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if ( vc == null )
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return null;
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return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model);
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return results;
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}
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/**
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@ -177,15 +183,20 @@ public class UnifiedGenotyperEngine {
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* @return the VariantContext object
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*/
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public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel( tracker, refContext, rawContext );
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if( model == null )
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final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
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if ( models.isEmpty() ) {
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return null;
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}
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Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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if ( stratifiedContexts == null )
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return null;
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for ( final GenotypeLikelihoodsCalculationModel.Model model : models ) {
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final Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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// return the first valid one we encounter
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if ( stratifiedContexts != null )
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return calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
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return calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
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}
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return null;
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}
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/**
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@ -198,17 +209,18 @@ public class UnifiedGenotyperEngine {
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* @return the VariantCallContext object
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*/
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public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, VariantContext vc) {
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final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel(tracker, refContext, rawContext );
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if( model == null ) {
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final List<GenotypeLikelihoodsCalculationModel.Model> models = getGLModelsToUse(tracker, refContext, rawContext);
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if ( models.isEmpty() ) {
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return null;
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}
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Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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// return the first one
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final GenotypeLikelihoodsCalculationModel.Model model = models.get(0);
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final Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
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return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model);
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}
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// ---------------------------------------------------------------------------------------------------------
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//
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// Private implementation helpers
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@ -243,13 +255,9 @@ public class UnifiedGenotyperEngine {
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vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles).make();
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}
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if ( annotationEngine != null ) {
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if ( annotationEngine != null && rawContext.hasBasePileup() ) {
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// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
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ReadBackedPileup pileup = null;
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if (rawContext.hasExtendedEventPileup())
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pileup = rawContext.getExtendedEventPileup();
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else if (rawContext.hasBasePileup())
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pileup = rawContext.getBasePileup();
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final ReadBackedPileup pileup = rawContext.getBasePileup();
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stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
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vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
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@ -409,13 +417,9 @@ public class UnifiedGenotyperEngine {
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builder.attributes(attributes);
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VariantContext vcCall = builder.make();
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if ( annotationEngine != null && !limitedContext ) {
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if ( annotationEngine != null && !limitedContext && rawContext.hasBasePileup() ) {
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// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
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ReadBackedPileup pileup = null;
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if (rawContext.hasExtendedEventPileup())
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pileup = rawContext.getExtendedEventPileup();
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else if (rawContext.hasBasePileup())
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pileup = rawContext.getBasePileup();
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final ReadBackedPileup pileup = rawContext.getBasePileup();
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stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
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vcCall = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, vcCall);
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@ -432,52 +436,33 @@ public class UnifiedGenotyperEngine {
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private Map<String, AlignmentContext> getFilteredAndStratifiedContexts(UnifiedArgumentCollection UAC, ReferenceContext refContext, AlignmentContext rawContext, final GenotypeLikelihoodsCalculationModel.Model model) {
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Map<String, AlignmentContext> stratifiedContexts = null;
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if ( !BaseUtils.isRegularBase( refContext.getBase() ) )
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if ( !BaseUtils.isRegularBase(refContext.getBase()) || !rawContext.hasBasePileup() )
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return null;
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if ( model.name().toUpperCase().contains("INDEL")) {
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Map<String, AlignmentContext> stratifiedContexts = null;
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if (UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
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// regular pileup in this case
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ReadBackedPileup pileup = rawContext.getBasePileup() .getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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if ( model.name().contains("INDEL") ) {
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// don't call when there is no coverage
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if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
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return null;
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final ReadBackedPileup pileup = rawContext.getBasePileup().getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
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// don't call when there is no coverage
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if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
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||||
return null;
|
||||
|
||||
// stratify the AlignmentContext and cut by sample
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
|
||||
// stratify the AlignmentContext and cut by sample
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
|
||||
|
||||
} else {
|
||||
|
||||
// todo - tmp will get rid of extended events so this wont be needed
|
||||
if (!rawContext.hasExtendedEventPileup())
|
||||
return null;
|
||||
ReadBackedExtendedEventPileup rawPileup = rawContext.getExtendedEventPileup();
|
||||
|
||||
// filter the context based on min mapping quality
|
||||
ReadBackedExtendedEventPileup pileup = rawPileup.getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
|
||||
|
||||
// don't call when there is no coverage
|
||||
if ( pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES )
|
||||
return null;
|
||||
|
||||
// stratify the AlignmentContext and cut by sample
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
|
||||
}
|
||||
} else if ( model.name().toUpperCase().contains("SNP") ) {
|
||||
} else if ( model.name().contains("SNP") ) {
|
||||
|
||||
// stratify the AlignmentContext and cut by sample
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
|
||||
|
||||
if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
|
||||
if ( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
|
||||
int numDeletions = 0;
|
||||
for( final PileupElement p : rawContext.getBasePileup() ) {
|
||||
if( p.isDeletion() ) { numDeletions++; }
|
||||
for ( final PileupElement p : rawContext.getBasePileup() ) {
|
||||
if ( p.isDeletion() )
|
||||
numDeletions++;
|
||||
}
|
||||
if( ((double) numDeletions) / ((double) rawContext.getBasePileup().getNumberOfElements()) > UAC.MAX_DELETION_FRACTION ) {
|
||||
if ( ((double) numDeletions) / ((double) rawContext.getBasePileup().getNumberOfElements()) > UAC.MAX_DELETION_FRACTION ) {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
|
@ -516,12 +501,10 @@ public class UnifiedGenotyperEngine {
|
|||
|
||||
int depth = 0;
|
||||
|
||||
if (isCovered) {
|
||||
if ( isCovered ) {
|
||||
AlignmentContext context = contexts.get(sample);
|
||||
if (context.hasBasePileup())
|
||||
if ( context.hasBasePileup() )
|
||||
depth = context.getBasePileup().depthOfCoverage();
|
||||
else if (context.hasExtendedEventPileup())
|
||||
depth = context.getExtendedEventPileup().depthOfCoverage();
|
||||
}
|
||||
|
||||
P_of_ref *= 1.0 - (theta / 2.0) * getRefBinomialProb(depth);
|
||||
|
|
@ -576,52 +559,48 @@ public class UnifiedGenotyperEngine {
|
|||
(UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && QualityUtils.phredScaleErrorRate(PofF) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
|
||||
}
|
||||
|
||||
// decide whether we are currently processing SNPs, indels, or neither
|
||||
private GenotypeLikelihoodsCalculationModel.Model getCurrentGLModel(final RefMetaDataTracker tracker, final ReferenceContext refContext,
|
||||
final AlignmentContext rawContext ) {
|
||||
if (rawContext.hasExtendedEventPileup() ) {
|
||||
// todo - remove this code
|
||||
if ((UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH || UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.INDEL) &&
|
||||
(UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) )
|
||||
return GenotypeLikelihoodsCalculationModel.Model.INDEL;
|
||||
}
|
||||
else {
|
||||
// no extended event pileup
|
||||
// decide whether we are currently processing SNPs, indels, neither, or both
|
||||
private List<GenotypeLikelihoodsCalculationModel.Model> getGLModelsToUse(final RefMetaDataTracker tracker,
|
||||
final ReferenceContext refContext,
|
||||
final AlignmentContext rawContext) {
|
||||
|
||||
final List<GenotypeLikelihoodsCalculationModel.Model> models = new ArrayList<GenotypeLikelihoodsCalculationModel.Model>(2);
|
||||
|
||||
if ( rawContext.hasBasePileup() ) {
|
||||
// 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) {
|
||||
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
|
||||
if (vcInput == null)
|
||||
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 )
|
||||
return null;
|
||||
|
||||
// todo - no support to genotype MNP's yet
|
||||
if (vcInput.isMNP())
|
||||
return null;
|
||||
|
||||
if (vcInput.isSNP()) {
|
||||
if ( vcInput.isSNP() ) {
|
||||
// ignore SNPs if the user chose INDEL mode only
|
||||
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
|
||||
return GenotypeLikelihoodsCalculationModel.Model.SNP;
|
||||
else if ( UAC.GLmodel.name().toUpperCase().contains("SNP"))
|
||||
return UAC.GLmodel;
|
||||
else
|
||||
// ignore SNP's if user chose INDEL mode
|
||||
return null;
|
||||
models.add(GenotypeLikelihoodsCalculationModel.Model.SNP);
|
||||
else if ( UAC.GLmodel.name().toUpperCase().contains("SNP") )
|
||||
models.add(UAC.GLmodel);
|
||||
}
|
||||
else if ((vcInput.isIndel() || vcInput.isMixed())) {
|
||||
else if ( vcInput.isIndel() || vcInput.isMixed() ) {
|
||||
// ignore INDELs if the user chose SNP mode only
|
||||
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
|
||||
return GenotypeLikelihoodsCalculationModel.Model.INDEL;
|
||||
models.add(GenotypeLikelihoodsCalculationModel.Model.INDEL);
|
||||
else if (UAC.GLmodel.name().toUpperCase().contains("INDEL"))
|
||||
return UAC.GLmodel;
|
||||
models.add(UAC.GLmodel);
|
||||
}
|
||||
// No support for other types yet
|
||||
}
|
||||
else {
|
||||
// todo - this assumes SNP's take priority when BOTH is selected, should do a smarter way once extended events are removed
|
||||
if( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH )
|
||||
return GenotypeLikelihoodsCalculationModel.Model.SNP;
|
||||
else if (UAC.GLmodel.name().toUpperCase().contains("SNP") || UAC.GLmodel.name().toUpperCase().contains("INDEL"))
|
||||
return UAC.GLmodel;
|
||||
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH ) {
|
||||
models.add(GenotypeLikelihoodsCalculationModel.Model.SNP);
|
||||
models.add(GenotypeLikelihoodsCalculationModel.Model.INDEL);
|
||||
}
|
||||
else {
|
||||
models.add(UAC.GLmodel);
|
||||
}
|
||||
}
|
||||
}
|
||||
return null;
|
||||
|
||||
return models;
|
||||
}
|
||||
|
||||
protected static void computeAlleleFrequencyPriors(final int N, final double[] priors, final double theta) {
|
||||
|
|
@ -668,24 +647,21 @@ public class UnifiedGenotyperEngine {
|
|||
else throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
|
||||
}
|
||||
|
||||
private static Map<String,GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
|
||||
private static Map<String, GenotypeLikelihoodsCalculationModel> getGenotypeLikelihoodsCalculationObject(Logger logger, UnifiedArgumentCollection UAC) {
|
||||
|
||||
|
||||
Map<String, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<String, GenotypeLikelihoodsCalculationModel>();
|
||||
// GenotypeLikelihoodsCalculationModel.Model.
|
||||
List<Class<? extends GenotypeLikelihoodsCalculationModel>> glmClasses = new PluginManager<GenotypeLikelihoodsCalculationModel>(GenotypeLikelihoodsCalculationModel.class).getPlugins();
|
||||
final Map<String, GenotypeLikelihoodsCalculationModel> glcm = new HashMap<String, GenotypeLikelihoodsCalculationModel>();
|
||||
final List<Class<? extends GenotypeLikelihoodsCalculationModel>> glmClasses = new PluginManager<GenotypeLikelihoodsCalculationModel>(GenotypeLikelihoodsCalculationModel.class).getPlugins();
|
||||
|
||||
for (int i = 0; i < glmClasses.size(); i++) {
|
||||
Class<? extends GenotypeLikelihoodsCalculationModel> glmClass = glmClasses.get(i);
|
||||
String key = glmClass.getSimpleName().replaceAll("GenotypeLikelihoodsCalculationModel","").toUpperCase();
|
||||
//System.out.println("KEY:"+key+"\t" + glmClass.getSimpleName());
|
||||
final Class<? extends GenotypeLikelihoodsCalculationModel> glmClass = glmClasses.get(i);
|
||||
final String key = glmClass.getSimpleName().replaceAll("GenotypeLikelihoodsCalculationModel","").toUpperCase();
|
||||
try {
|
||||
Object args[] = new Object[]{UAC,logger};
|
||||
Constructor c = glmClass.getDeclaredConstructor(UnifiedArgumentCollection.class, Logger.class);
|
||||
final Object args[] = new Object[]{UAC,logger};
|
||||
final Constructor c = glmClass.getDeclaredConstructor(UnifiedArgumentCollection.class, Logger.class);
|
||||
glcm.put(key, (GenotypeLikelihoodsCalculationModel)c.newInstance(args));
|
||||
}
|
||||
catch (Exception e) {
|
||||
throw new UserException("Incorrect specification for argument glm:"+UAC.GLmodel+e.getMessage());
|
||||
throw new UserException("The likelihoods model provided for the -glm argument (" + UAC.GLmodel + ") is not a valid option: " + e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -719,7 +695,7 @@ public class UnifiedGenotyperEngine {
|
|||
VariantContext vc = null;
|
||||
|
||||
// search for usable record
|
||||
for( final VariantContext vc_input : tracker.getValues(allelesBinding, loc) ) {
|
||||
for ( final VariantContext vc_input : tracker.getValues(allelesBinding, loc) ) {
|
||||
if ( vc_input != null && ! vc_input.isFiltered() && (! requireSNP || vc_input.isSNP() )) {
|
||||
if ( vc == null ) {
|
||||
vc = vc_input;
|
||||
|
|
|
|||
|
|
@ -379,12 +379,12 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
|
|||
|
||||
VariantCallContext call;
|
||||
if ( vcComp.isSNP() ) {
|
||||
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
|
||||
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
|
||||
} else if ( vcComp.isIndel() ) {
|
||||
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
|
||||
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
|
||||
} else if ( bamIsTruth ) {
|
||||
// assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
|
||||
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
|
||||
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0);
|
||||
} else {
|
||||
logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
|
||||
return counter;
|
||||
|
|
|
|||
Loading…
Reference in New Issue