Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Ryan Poplin
commit
dbff84c54e
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@ -90,7 +90,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
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|||
}
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// todo -- actually care about indel length from the pileup (agnostic at the moment)
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int refCount = indelPileup.size();
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int altCount = vc.isInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
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||||
int altCount = vc.isSimpleInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
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||||
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||||
if ( refCount + altCount == 0 ) {
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continue;
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|
|
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|||
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@ -79,7 +79,7 @@ public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnot
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GenomeLoc locus = ref.getLocus();
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GenomeLoc window = ref.getWindow();
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int refBasePos = (int) (locus.getStart() - window.getStart())+1;
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if ( vc.isDeletion() ) {
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if ( vc.isSimpleDeletion() ) {
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// check that deleted bases are the same
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byte dBase = bases[refBasePos];
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for ( int i = 0; i < vc.getReference().length(); i ++ ) {
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|
|
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|
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@ -36,9 +36,9 @@ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnota
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if (!vc.isBiallelic())
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type = "MULTIALLELIC_INDEL";
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else {
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if (vc.isInsertion())
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if (vc.isSimpleInsertion())
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type = "INS.";
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else if (vc.isDeletion())
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else if (vc.isSimpleDeletion())
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type = "DEL.";
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else
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type = "OTHER.";
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|
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@ -101,11 +101,11 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
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if ( vc.isFiltered() )
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continue;
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if ( vc.isDeletion()) {
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if ( vc.isSimpleDeletion()) {
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deletionBasesRemaining = vc.getReference().length();
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// delete the next n bases, not this one
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
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} else if ( vc.isInsertion()) {
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} else if ( vc.isSimpleInsertion()) {
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return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
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} else if (vc.isSNP()) {
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return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());
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|
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@ -886,7 +886,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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for ( VariantContext knownIndel : knownIndelsToTry ) {
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if ( knownIndel == null || !knownIndel.isIndel() || knownIndel.isComplexIndel() )
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continue;
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byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
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byte[] indelStr = knownIndel.isSimpleInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
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int start = knownIndel.getStart() - leftmostIndex + 1;
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Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel);
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if ( c != null )
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@ -1088,11 +1088,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
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if ( indexOnRef > 0 )
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cigar.add(new CigarElement(indexOnRef, CigarOperator.M));
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if ( indel.isDeletion() ) {
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if ( indel.isSimpleDeletion() ) {
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refIdx += indelStr.length;
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cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
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}
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else if ( indel.isInsertion() ) {
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else if ( indel.isSimpleInsertion() ) {
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for ( byte b : indelStr )
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sb.append((char)b);
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cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
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@ -178,7 +178,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
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switch ( vc.getType() ) {
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case INDEL:
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hasIndel = true;
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if ( vc.isInsertion() )
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if ( vc.isSimpleInsertion() )
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hasInsertion = true;
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break;
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case SNP:
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@ -187,7 +187,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
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case MIXED:
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hasPointEvent = true;
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hasIndel = true;
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if ( vc.isInsertion() )
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if ( vc.isSimpleInsertion() )
|
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hasInsertion = true;
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break;
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default:
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|
|
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@ -250,17 +250,17 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
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} else /* (mask != null && validate == null ) */ {
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if ( ! mask.isSNP() && ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphic() )) {
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logger.warn("Mask Variant Context on the following warning line is not a SNP. Currently we can only mask out SNPs. This probe will not be designed.");
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logger.warn(String.format("%s:%d-%d\t%s\t%s",mask.getChr(),mask.getStart(),mask.getEnd(),mask.isInsertion() ? "INS" : "DEL", Utils.join(",",mask.getAlleles())));
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logger.warn(String.format("%s:%d-%d\t%s\t%s",mask.getChr(),mask.getStart(),mask.getEnd(),mask.isSimpleInsertion() ? "INS" : "DEL", Utils.join(",",mask.getAlleles())));
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||||
sequenceInvalid = true;
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||||
invReason.add(mask.isInsertion() ? "INSERTION" : "DELETION");
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invReason.add(mask.isSimpleInsertion() ? "INSERTION" : "DELETION");
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// note: indelCounter could be > 0 (could have small deletion within larger one). This always selects
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// the larger event.
|
||||
int indelCounterNew = mask.isInsertion() ? 2 : mask.getEnd()-mask.getStart();
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||||
int indelCounterNew = mask.isSimpleInsertion() ? 2 : mask.getEnd()-mask.getStart();
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if ( indelCounterNew > indelCounter ) {
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||||
indelCounter = indelCounterNew;
|
||||
}
|
||||
//sequence.append((char) ref.getBase());
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//sequence.append(mask.isInsertion() ? 'I' : 'D');
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//sequence.append(mask.isSimpleInsertion() ? 'I' : 'D');
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||||
sequence.append("N");
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indelCounter--;
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rawSequence.append(Character.toUpperCase((char) ref.getBase()));
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|
|
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@ -311,7 +311,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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|||
// for each comp track
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for ( final RodBinding<VariantContext> compRod : comps ) {
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// no sample stratification for comps
|
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final Set<VariantContext> compSet = compVCs.get(compRod) == null ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
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final HashMap<String, Set<VariantContext>> compSetHash = compVCs.get(compRod);
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||||
final Set<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
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||||
|
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// find the comp
|
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final VariantContext comp = findMatchingComp(eval, compSet);
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|
|
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@ -39,8 +39,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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public long nInsertions = 0;
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@DataPoint(description = "Number of deletions")
|
||||
public long nDeletions = 0;
|
||||
@DataPoint(description = "Number of complex loci")
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@DataPoint(description = "Number of complex indels")
|
||||
public long nComplex = 0;
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||||
@DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
|
||||
public long nMixed = 0;
|
||||
|
||||
|
||||
@DataPoint(description = "Number of no calls loci")
|
||||
|
|
@ -113,11 +115,15 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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|||
if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
|
||||
break;
|
||||
case INDEL:
|
||||
if (vc1.isInsertion()) nInsertions++;
|
||||
else nDeletions++;
|
||||
if (vc1.isSimpleInsertion())
|
||||
nInsertions++;
|
||||
else if (vc1.isSimpleDeletion())
|
||||
nDeletions++;
|
||||
else
|
||||
nComplex++;
|
||||
break;
|
||||
case MIXED:
|
||||
nComplex++;
|
||||
nMixed++;
|
||||
break;
|
||||
default:
|
||||
throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
|
||||
|
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@ -180,8 +186,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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|||
heterozygosity = perLocusRate(nHets);
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heterozygosityPerBp = perLocusRInverseRate(nHets);
|
||||
hetHomRatio = ratio(nHets, nHomVar);
|
||||
indelRate = perLocusRate(nDeletions + nInsertions);
|
||||
indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions);
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||||
indelRate = perLocusRate(nDeletions + nInsertions + nComplex);
|
||||
indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions + nComplex);
|
||||
deletionInsertionRatio = ratio(nDeletions, nInsertions);
|
||||
}
|
||||
}
|
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@ -96,9 +96,9 @@ public class IndelLengthHistogram extends VariantEvaluator {
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}
|
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|
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if ( vc1.isIndel() ) {
|
||||
if ( vc1.isInsertion() ) {
|
||||
if ( vc1.isSimpleInsertion() ) {
|
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indelHistogram.update(vc1.getAlternateAllele(0).length());
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} else if ( vc1.isDeletion() ) {
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} else if ( vc1.isSimpleDeletion() ) {
|
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indelHistogram.update(-vc1.getReference().length());
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} else {
|
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throw new ReviewedStingException("Indel type that is not insertion or deletion.");
|
||||
|
|
|
|||
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@ -1,221 +0,0 @@
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|||
package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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||||
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||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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||||
import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
||||
/*
|
||||
* Copyright (c) 2010 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
/**
|
||||
* @author delangel
|
||||
* @since Apr 11, 2010
|
||||
*/
|
||||
|
||||
@Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count")
|
||||
public class IndelMetricsByAC extends VariantEvaluator {
|
||||
// a mapping from quality score histogram bin to Ti/Tv ratio
|
||||
@DataPoint(description = "Indel Metrics by allele count")
|
||||
IndelMetricsByAc metrics = null;
|
||||
|
||||
int numSamples = 0;
|
||||
|
||||
public void initialize(VariantEvalWalker walker) {
|
||||
numSamples = walker.getNumSamples();
|
||||
}
|
||||
|
||||
//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
|
||||
//AlleleCountStats alleleCountStats = null;
|
||||
private static final int INDEL_SIZE_LIMIT = 100;
|
||||
private static final int NUM_SCALAR_COLUMNS = 6;
|
||||
static int len2Index(int ind) {
|
||||
return ind+INDEL_SIZE_LIMIT;
|
||||
}
|
||||
|
||||
static int index2len(int ind) {
|
||||
return ind-INDEL_SIZE_LIMIT-NUM_SCALAR_COLUMNS;
|
||||
}
|
||||
|
||||
protected final static String[] METRIC_COLUMNS;
|
||||
static {
|
||||
METRIC_COLUMNS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
|
||||
METRIC_COLUMNS[0] = "AC";
|
||||
METRIC_COLUMNS[1] = "nIns";
|
||||
METRIC_COLUMNS[2] = "nDels";
|
||||
METRIC_COLUMNS[3] = "n";
|
||||
METRIC_COLUMNS[4] = "nComplex";
|
||||
METRIC_COLUMNS[5] = "nLong";
|
||||
|
||||
for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
|
||||
METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
|
||||
}
|
||||
|
||||
class IndelMetricsAtAC {
|
||||
public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong;
|
||||
public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1];
|
||||
|
||||
public IndelMetricsAtAC(int ac) { this.ac = ac; }
|
||||
|
||||
public void update(VariantContext eval) {
|
||||
int eventLength = 0;
|
||||
if ( eval.isInsertion() ) {
|
||||
eventLength = eval.getAlternateAllele(0).length();
|
||||
nIns++;
|
||||
} else if ( eval.isDeletion() ) {
|
||||
eventLength = -eval.getReference().length();
|
||||
nDel++;
|
||||
}
|
||||
else {
|
||||
nComplex++;
|
||||
}
|
||||
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT)
|
||||
sizeCount[len2Index(eventLength)]++;
|
||||
else
|
||||
nLong++;
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
// corresponding to METRIC_COLUMNS
|
||||
public String getColumn(int i) {
|
||||
if (i >= NUM_SCALAR_COLUMNS && i <=NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT)
|
||||
return String.valueOf(sizeCount[i-NUM_SCALAR_COLUMNS]);
|
||||
|
||||
switch (i) {
|
||||
case 0: return String.valueOf(ac);
|
||||
case 1: return String.valueOf(nIns);
|
||||
case 2: return String.valueOf(nDel);
|
||||
case 3: return String.valueOf(nIns + nDel);
|
||||
case 4: return String.valueOf(nComplex);
|
||||
case 5: return String.valueOf(nLong);
|
||||
|
||||
default:
|
||||
throw new ReviewedStingException("Unexpected column " + i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
class IndelMetricsByAc implements TableType {
|
||||
ArrayList<IndelMetricsAtAC> metrics = new ArrayList<IndelMetricsAtAC>();
|
||||
Object[] rows = null;
|
||||
|
||||
public IndelMetricsByAc( int nchromosomes ) {
|
||||
rows = new Object[nchromosomes+1];
|
||||
metrics = new ArrayList<IndelMetricsAtAC>(nchromosomes+1);
|
||||
for ( int i = 0; i < nchromosomes + 1; i++ ) {
|
||||
metrics.add(new IndelMetricsAtAC(i));
|
||||
rows[i] = "ac" + i;
|
||||
}
|
||||
}
|
||||
|
||||
public Object[] getRowKeys() {
|
||||
return rows;
|
||||
}
|
||||
|
||||
public Object[] getColumnKeys() {
|
||||
return METRIC_COLUMNS;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return "IndelMetricsByAc";
|
||||
}
|
||||
|
||||
//
|
||||
public String getCell(int ac, int y) {
|
||||
return metrics.get(ac).getColumn(y);
|
||||
}
|
||||
|
||||
public String toString() {
|
||||
return "";
|
||||
}
|
||||
|
||||
public void incrValue( VariantContext eval ) {
|
||||
int ac = -1;
|
||||
|
||||
if ( eval.hasGenotypes() )
|
||||
ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
|
||||
else if ( eval.hasAttribute("AC") ) {
|
||||
ac = Integer.valueOf(eval.getAttributeAsString("AC"));
|
||||
}
|
||||
|
||||
if ( ac != -1 )
|
||||
metrics.get(ac).update(eval);
|
||||
}
|
||||
}
|
||||
|
||||
//public IndelMetricsByAC(VariantEvalWalker parent) {
|
||||
//super(parent);
|
||||
// don't do anything
|
||||
//}
|
||||
|
||||
public String getName() {
|
||||
return "IndelMetricsByAC";
|
||||
}
|
||||
|
||||
public int getComparisonOrder() {
|
||||
return 1; // we only need to see each eval track
|
||||
}
|
||||
|
||||
public boolean enabled() {
|
||||
return true;
|
||||
}
|
||||
|
||||
public String toString() {
|
||||
return getName();
|
||||
}
|
||||
|
||||
public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
final String interesting = null;
|
||||
|
||||
if (eval != null ) {
|
||||
if ( metrics == null ) {
|
||||
int nSamples = numSamples;
|
||||
//int nSamples = 2;
|
||||
if ( nSamples != -1 )
|
||||
metrics = new IndelMetricsByAc(2 * nSamples);
|
||||
}
|
||||
|
||||
if ( eval.isIndel() && eval.isBiallelic() &&
|
||||
metrics != null ) {
|
||||
metrics.incrValue(eval);
|
||||
}
|
||||
}
|
||||
|
||||
return interesting; // This module doesn't capture any interesting sites, so return null
|
||||
}
|
||||
|
||||
//public void finalizeEvaluation() {
|
||||
//
|
||||
//}
|
||||
}
|
||||
|
|
@ -44,7 +44,7 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
@DataPoint(description = "Indel Statistics")
|
||||
IndelStats indelStats = null;
|
||||
|
||||
@DataPoint(description = "Indel Classification")
|
||||
// @DataPoint(description = "Indel Classification")
|
||||
IndelClasses indelClasses = null;
|
||||
|
||||
int numSamples = 0;
|
||||
|
|
@ -57,13 +57,13 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
private static final int IND_HET = 0;
|
||||
private static final int IND_INS = 1;
|
||||
private static final int IND_DEL = 2;
|
||||
private static final int IND_AT_CG_RATIO = 3;
|
||||
private static final int IND_COMPLEX = 3;
|
||||
private static final int IND_HET_INS = 4;
|
||||
private static final int IND_HOM_INS = 5;
|
||||
private static final int IND_HET_DEL = 6;
|
||||
private static final int IND_HOM_DEL = 7;
|
||||
private static final int IND_HOM_REF = 8;
|
||||
private static final int IND_COMPLEX = 9;
|
||||
private static final int IND_MIXED = 9;
|
||||
private static final int IND_LONG = 10;
|
||||
private static final int IND_AT_EXP = 11;
|
||||
private static final int IND_CG_EXP = 12;
|
||||
|
|
@ -79,15 +79,14 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
}
|
||||
|
||||
static class IndelStats implements TableType {
|
||||
protected final static String ALL_SAMPLES_KEY = "allSamples";
|
||||
protected final static String[] COLUMN_KEYS;
|
||||
protected final static String[] COLUMN_KEYS;
|
||||
|
||||
static {
|
||||
COLUMN_KEYS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
|
||||
COLUMN_KEYS[0] = "heterozygosity";
|
||||
COLUMN_KEYS[1] = "insertions";
|
||||
COLUMN_KEYS[2] = "deletions";
|
||||
COLUMN_KEYS[3] = "AT_CG_expansion_ratio";
|
||||
COLUMN_KEYS[3] = "complex";
|
||||
COLUMN_KEYS[4] = "het_insertions";
|
||||
COLUMN_KEYS[5] = "homozygous_insertions";
|
||||
COLUMN_KEYS[6] = "het_deletions";
|
||||
|
|
@ -104,13 +103,10 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
}
|
||||
|
||||
// map of sample to statistics
|
||||
protected final HashMap<String, int[]> indelSummary = new HashMap<String, int[]>();
|
||||
protected final int[] indelSummary;
|
||||
|
||||
public IndelStats(final VariantContext vc) {
|
||||
indelSummary.put(ALL_SAMPLES_KEY, new int[COLUMN_KEYS.length]);
|
||||
for( final String sample : vc.getGenotypes().keySet() ) {
|
||||
indelSummary.put(sample, new int[COLUMN_KEYS.length]);
|
||||
}
|
||||
indelSummary = new int[COLUMN_KEYS.length];
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -118,19 +114,10 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
* @return one row per sample
|
||||
*/
|
||||
public Object[] getRowKeys() {
|
||||
return indelSummary.keySet().toArray(new String[indelSummary.size()]);
|
||||
return new String[]{"all"};
|
||||
}
|
||||
public Object getCell(int x, int y) {
|
||||
final Object[] rowKeys = getRowKeys();
|
||||
if (y == IND_AT_CG_RATIO) {
|
||||
|
||||
int at = indelSummary.get(rowKeys[x])[IND_AT_EXP];
|
||||
int cg = indelSummary.get(rowKeys[x])[IND_CG_EXP];
|
||||
return String.format("%4.2f",((double)at) / (Math.max(cg, 1)));
|
||||
}
|
||||
else
|
||||
return String.format("%d",indelSummary.get(rowKeys[x])[y]);
|
||||
|
||||
return String.format("%d",indelSummary[y]);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -160,96 +147,49 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
int eventLength = 0;
|
||||
boolean isInsertion = false, isDeletion = false;
|
||||
|
||||
if ( vc.isInsertion() ) {
|
||||
if ( vc.isSimpleInsertion() ) {
|
||||
eventLength = vc.getAlternateAllele(0).length();
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_INS]++;
|
||||
indelSummary[IND_INS]++;
|
||||
isInsertion = true;
|
||||
} else if ( vc.isDeletion() ) {
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_DEL]++;
|
||||
} else if ( vc.isSimpleDeletion() ) {
|
||||
indelSummary[IND_DEL]++;
|
||||
eventLength = -vc.getReference().length();
|
||||
isDeletion = true;
|
||||
}
|
||||
else {
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_COMPLEX]++;
|
||||
else if (vc.isComplexIndel()) {
|
||||
indelSummary[IND_COMPLEX]++;
|
||||
}
|
||||
else if (vc.isMixed())
|
||||
indelSummary[IND_MIXED]++;
|
||||
|
||||
if (IndelUtils.isATExpansion(vc,ref))
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_AT_EXP]++;
|
||||
indelSummary[IND_AT_EXP]++;
|
||||
if (IndelUtils.isCGExpansion(vc,ref))
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_CG_EXP]++;
|
||||
indelSummary[IND_CG_EXP]++;
|
||||
|
||||
// make sure event doesn't overstep array boundaries
|
||||
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[len2Index(eventLength)]++;
|
||||
if (eventLength % 3 != 0)
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_FRAMESHIFT]++;
|
||||
}
|
||||
else
|
||||
indelSummary.get(ALL_SAMPLES_KEY)[IND_LONG]++;
|
||||
|
||||
|
||||
for( final String sample : vc.getGenotypes().keySet() ) {
|
||||
if ( indelSummary.containsKey(sample) ) {
|
||||
Genotype g = vc.getGenotype(sample);
|
||||
boolean isVariant = (g.isCalled() && !g.isHomRef());
|
||||
if (isVariant) {
|
||||
// update ins/del count
|
||||
if (isInsertion) {
|
||||
indelSummary.get(sample)[IND_INS]++;
|
||||
}
|
||||
else if (isDeletion)
|
||||
indelSummary.get(sample)[IND_DEL]++;
|
||||
else
|
||||
indelSummary.get(sample)[IND_COMPLEX]++;
|
||||
|
||||
// update histogram
|
||||
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
|
||||
indelSummary.get(sample)[len2Index(eventLength)]++;
|
||||
if (eventLength % 3 != 0)
|
||||
indelSummary.get(sample)[IND_FRAMESHIFT]++;
|
||||
}
|
||||
else
|
||||
indelSummary.get(sample)[IND_LONG]++;
|
||||
|
||||
if (g.isHet())
|
||||
if (isInsertion)
|
||||
indelSummary.get(sample)[IND_HET_INS]++;
|
||||
else if (isDeletion)
|
||||
indelSummary.get(sample)[IND_HET_DEL]++;
|
||||
else
|
||||
if (isInsertion)
|
||||
indelSummary.get(sample)[IND_HOM_INS]++;
|
||||
else if (isDeletion)
|
||||
indelSummary.get(sample)[IND_HOM_DEL]++;
|
||||
|
||||
if (IndelUtils.isATExpansion(vc,ref))
|
||||
indelSummary.get(sample)[IND_AT_EXP]++;
|
||||
if (IndelUtils.isCGExpansion(vc,ref))
|
||||
indelSummary.get(sample)[IND_CG_EXP]++;
|
||||
|
||||
|
||||
}
|
||||
else
|
||||
indelSummary.get(sample)[IND_HOM_REF]++;
|
||||
if (vc.isSimpleDeletion() || vc.isSimpleInsertion()) {
|
||||
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
|
||||
indelSummary[len2Index(eventLength)]++;
|
||||
if (eventLength % 3 != 0)
|
||||
indelSummary[IND_FRAMESHIFT]++;
|
||||
}
|
||||
else
|
||||
indelSummary[IND_LONG]++;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
static class IndelClasses implements TableType {
|
||||
protected final static String ALL_SAMPLES_KEY = "allSamples";
|
||||
protected final static String[] columnNames = IndelUtils.getIndelClassificationNames();
|
||||
|
||||
|
||||
// map of sample to statistics
|
||||
protected final HashMap<String, int[]> indelClassSummary = new HashMap<String, int[]>();
|
||||
protected final int[] indelClassSummary;
|
||||
|
||||
public IndelClasses(final VariantContext vc) {
|
||||
indelClassSummary.put(ALL_SAMPLES_KEY, new int[columnNames.length]);
|
||||
for( final String sample : vc.getGenotypes().keySet() ) {
|
||||
indelClassSummary.put(sample, new int[columnNames.length]);
|
||||
}
|
||||
indelClassSummary = new int[columnNames.length];
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -257,11 +197,10 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
* @return one row per sample
|
||||
*/
|
||||
public Object[] getRowKeys() {
|
||||
return indelClassSummary.keySet().toArray(new String[indelClassSummary.size()]);
|
||||
return new String[]{"all"};
|
||||
}
|
||||
public Object getCell(int x, int y) {
|
||||
final Object[] rowKeys = getRowKeys();
|
||||
return String.format("%d",indelClassSummary.get(rowKeys[x])[y]);
|
||||
return String.format("%d",indelClassSummary[y]);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -285,18 +224,7 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
}
|
||||
|
||||
private void incrementSampleStat(VariantContext vc, int index) {
|
||||
indelClassSummary.get(ALL_SAMPLES_KEY)[index]++;
|
||||
for( final String sample : vc.getGenotypes().keySet() ) {
|
||||
if ( indelClassSummary.containsKey(sample) ) {
|
||||
Genotype g = vc.getGenotype(sample);
|
||||
boolean isVariant = (g.isCalled() && !g.isHomRef());
|
||||
if (isVariant)
|
||||
// update count
|
||||
indelClassSummary.get(sample)[index]++;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
indelClassSummary[index]++;
|
||||
}
|
||||
/*
|
||||
* increment the specified value
|
||||
|
|
@ -344,16 +272,13 @@ public class IndelStatistics extends VariantEvaluator {
|
|||
|
||||
if (eval != null ) {
|
||||
if ( indelStats == null ) {
|
||||
int nSamples = numSamples;
|
||||
|
||||
if ( nSamples != -1 )
|
||||
indelStats = new IndelStats(eval);
|
||||
indelStats = new IndelStats(eval);
|
||||
}
|
||||
if ( indelClasses == null ) {
|
||||
indelClasses = new IndelClasses(eval);
|
||||
}
|
||||
|
||||
if ( eval.isIndel() && eval.isBiallelic() ) {
|
||||
if ( eval.isIndel() || eval.isMixed() ) {
|
||||
if (indelStats != null )
|
||||
indelStats.incrValue(eval, ref);
|
||||
|
||||
|
|
|
|||
|
|
@ -347,9 +347,9 @@ public class VariantEvalUtils {
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
bindings.put(track, mapping);
|
||||
}
|
||||
|
||||
bindings.put(track, mapping);
|
||||
}
|
||||
|
||||
return bindings;
|
||||
|
|
|
|||
|
|
@ -133,7 +133,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
|
||||
// get the indel length
|
||||
int indelLength;
|
||||
if ( vc.isDeletion() )
|
||||
if ( vc.isSimpleDeletion() )
|
||||
indelLength = vc.getReference().length();
|
||||
else
|
||||
indelLength = vc.getAlternateAllele(0).length();
|
||||
|
|
@ -150,7 +150,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
// create a CIGAR string to represent the event
|
||||
ArrayList<CigarElement> elements = new ArrayList<CigarElement>();
|
||||
elements.add(new CigarElement(originalIndex, CigarOperator.M));
|
||||
elements.add(new CigarElement(indelLength, vc.isDeletion() ? CigarOperator.D : CigarOperator.I));
|
||||
elements.add(new CigarElement(indelLength, vc.isSimpleDeletion() ? CigarOperator.D : CigarOperator.I));
|
||||
elements.add(new CigarElement(refSeq.length - originalIndex, CigarOperator.M));
|
||||
Cigar originalCigar = new Cigar(elements);
|
||||
|
||||
|
|
@ -165,8 +165,8 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
|
||||
int indelIndex = originalIndex-difference;
|
||||
byte[] newBases = new byte[indelLength];
|
||||
System.arraycopy((vc.isDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength);
|
||||
Allele newAllele = Allele.create(newBases, vc.isDeletion());
|
||||
System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength);
|
||||
Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion());
|
||||
newVC = updateAllele(newVC, newAllele, refSeq[indelIndex-1]);
|
||||
|
||||
writer.add(newVC);
|
||||
|
|
@ -178,14 +178,14 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
}
|
||||
|
||||
private static byte[] makeHaplotype(VariantContext vc, byte[] ref, int indexOfRef, int indelLength) {
|
||||
byte[] hap = new byte[ref.length + (indelLength * (vc.isDeletion() ? -1 : 1))];
|
||||
byte[] hap = new byte[ref.length + (indelLength * (vc.isSimpleDeletion() ? -1 : 1))];
|
||||
|
||||
// add the bases before the indel
|
||||
System.arraycopy(ref, 0, hap, 0, indexOfRef);
|
||||
int currentPos = indexOfRef;
|
||||
|
||||
// take care of the indel
|
||||
if ( vc.isDeletion() ) {
|
||||
if ( vc.isSimpleDeletion() ) {
|
||||
indexOfRef += indelLength;
|
||||
} else {
|
||||
System.arraycopy(vc.getAlternateAllele(0).getBases(), 0, hap, currentPos, indelLength);
|
||||
|
|
|
|||
|
|
@ -209,7 +209,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
|
||||
*/
|
||||
@Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
|
||||
public Set<File> XLsampleFiles;
|
||||
public Set<File> XLsampleFiles = new HashSet<File>(0);
|
||||
|
||||
/**
|
||||
* Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
|
||||
|
|
@ -348,7 +348,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
samples.removeAll(XLsamplesFromFile);
|
||||
samples.removeAll(XLsampleNames);
|
||||
|
||||
if ( samples.size() == 0 )
|
||||
if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
|
||||
throw new UserException("All samples requested to be included were also requested to be excluded.");
|
||||
|
||||
for ( String sample : samples )
|
||||
|
|
|
|||
|
|
@ -137,11 +137,11 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
|
|||
Allele reportedRefAllele = vc.getReference();
|
||||
Allele observedRefAllele;
|
||||
// insertions
|
||||
if ( vc.isInsertion() ) {
|
||||
if ( vc.isSimpleInsertion() ) {
|
||||
observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
|
||||
}
|
||||
// deletions
|
||||
else if ( vc.isDeletion() || vc.isMixed() || vc.isMNP() ) {
|
||||
else if ( vc.isSimpleDeletion() || vc.isMixed() || vc.isMNP() ) {
|
||||
// we can't validate arbitrarily long deletions
|
||||
if ( reportedRefAllele.length() > 100 ) {
|
||||
logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));
|
||||
|
|
|
|||
|
|
@ -167,8 +167,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
|
|||
continue;
|
||||
|
||||
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
|
||||
alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
|
||||
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
|
||||
alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isSimpleInsertion()));
|
||||
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
|
||||
hapmap.setActualAlleles(alleleMap);
|
||||
|
||||
// also, use the correct positioning for insertions
|
||||
|
|
|
|||
|
|
@ -144,6 +144,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
} else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
|
||||
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, BAMIndex.BAMIndexSuffix, ".bam"));
|
||||
|
||||
} else if ((RodBinding.class.equals(argumentDefinition.argumentType) || RodBinding.class.equals(argumentDefinition.componentType)) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
|
||||
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION));
|
||||
|
||||
} else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
|
||||
return Collections.singletonList(new InputArgumentField(argumentDefinition));
|
||||
|
||||
|
|
@ -196,7 +199,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
}
|
||||
|
||||
// if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT)
|
||||
// Change intervals exclusize of intervalsString.
|
||||
// Change intervals exclusive of intervalsString.
|
||||
private static class IntervalFileArgumentField extends InputArgumentField {
|
||||
public IntervalFileArgumentField(ArgumentDefinition argumentDefinition) {
|
||||
super(argumentDefinition);
|
||||
|
|
@ -332,9 +335,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* The other extreme of a NamedRodBindingField, allows the user to specify the track name, track type, and the file.
|
||||
*/
|
||||
// Allows the user to specify the track name, track type, and the file.
|
||||
public static class RodBindArgumentField extends ArgumentDefinitionField {
|
||||
public RodBindArgumentField(ArgumentDefinition argumentDefinition) {
|
||||
super(argumentDefinition);
|
||||
|
|
@ -347,25 +348,28 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Named input_files.
|
||||
*/
|
||||
// Tagged input_files or other rods.
|
||||
public static class InputTaggedFileDefinitionField extends ArgumentDefinitionField {
|
||||
public InputTaggedFileDefinitionField(ArgumentDefinition argumentDefinition) {
|
||||
super(argumentDefinition);
|
||||
}
|
||||
@Override protected Class<?> getInnerType() { return null; } // TaggedFile does not need to be imported.
|
||||
@Override protected String getFieldType() { return "List[File]"; }
|
||||
@Override protected String getDefaultValue() { return "Nil"; }
|
||||
@Override protected String getFieldType() { return argumentDefinition.isMultiValued ? "List[File]" : "File"; }
|
||||
@Override protected String getDefaultValue() { return argumentDefinition.isMultiValued ? "Nil" : "_"; }
|
||||
@Override protected String getCommandLineTemplate() {
|
||||
return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
|
||||
if (argumentDefinition.isMultiValued) {
|
||||
return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
|
||||
} else if (!argumentDefinition.required) {
|
||||
return " + optional(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
|
||||
} else {
|
||||
return " + TaggedFile.formatCommandLine(\"%1$s\")(\"\", %3$s, \"\")";
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Adds optional inputs for the indexes of any bams or sams added to this function.
|
||||
*/
|
||||
// Adds optional inputs for the indexes of any rods added to this function.
|
||||
private static class InputIndexesArgumentField extends ArgumentField {
|
||||
private final boolean originalIsMultiValued;
|
||||
private final String indexFieldName;
|
||||
private final String originalFieldName;
|
||||
private final String indexSuffix;
|
||||
|
|
@ -374,14 +378,19 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
this(originalArgumentDefinition, indexSuffix, null);
|
||||
}
|
||||
public InputIndexesArgumentField(ArgumentDefinition originalArgumentDefinition, String indexSuffix, String originalSuffix) {
|
||||
this.indexFieldName = originalArgumentDefinition.fullName + "Indexes";
|
||||
this.originalIsMultiValued = originalArgumentDefinition.isMultiValued;
|
||||
this.indexFieldName = originalArgumentDefinition.fullName + "Index" + (originalIsMultiValued ? "es" : "");
|
||||
this.originalFieldName = originalArgumentDefinition.fullName;
|
||||
this.indexSuffix = indexSuffix;
|
||||
this.originalSuffix = originalSuffix;
|
||||
}
|
||||
@Override protected Class<? extends Annotation> getAnnotationIOClass() { return Input.class; }
|
||||
@Override public String getCommandLineAddition() { return ""; }
|
||||
@Override protected String getDoc() { return "Dependencies on any indexes of " + this.originalFieldName; }
|
||||
@Override protected String getDoc() {
|
||||
return originalIsMultiValued
|
||||
? "Dependencies on any indexes of " + this.originalFieldName
|
||||
: "Dependencies on the index of " + this.originalFieldName;
|
||||
}
|
||||
@Override protected String getFullName() { return this.indexFieldName; }
|
||||
@Override protected boolean isRequired() { return false; }
|
||||
@Override protected String getFieldType() { return "List[File]"; }
|
||||
|
|
@ -389,24 +398,41 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
@Override protected Class<?> getInnerType() { return File.class; }
|
||||
@Override protected String getRawFieldName() { return this.indexFieldName; }
|
||||
@Override protected String getFreezeFields() {
|
||||
if (originalSuffix == null) {
|
||||
return String.format(
|
||||
("%1$s ++= %2$s" +
|
||||
".filter(orig => orig != null)" +
|
||||
".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix);
|
||||
if (originalIsMultiValued) {
|
||||
if (originalSuffix == null) {
|
||||
return String.format(
|
||||
("%1$s ++= %2$s" +
|
||||
".filter(orig => orig != null)" +
|
||||
".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix);
|
||||
} else {
|
||||
return String.format(
|
||||
("%1$s ++= %2$s" +
|
||||
".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
|
||||
".flatMap(orig => Array(" +
|
||||
" new File(orig.getPath + \"%3$s\")," +
|
||||
" new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
|
||||
}
|
||||
} else {
|
||||
return String.format(
|
||||
("%1$s ++= %2$s" +
|
||||
".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
|
||||
".flatMap(orig => Array(" +
|
||||
" new File(orig.getPath + \"%3$s\")," +
|
||||
" new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
|
||||
if (originalSuffix == null) {
|
||||
return String.format(
|
||||
("if (%2$s != null)%n " +
|
||||
"%1$s :+= new File(%2$s.getPath + \"%3$s\")%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix);
|
||||
} else {
|
||||
return String.format(
|
||||
("if (%2$s != null && %2$s.getName.endsWith(\"%4$s\"))%n " +
|
||||
"%1$s ++= Array(" +
|
||||
" new File(%2$s.getPath + \"%3$s\")," +
|
||||
" new File(%2$s.getPath.stripSuffix(\"%4$s\") + \"%3$s\") )%n"),
|
||||
indexFieldName, originalFieldName, indexSuffix, originalSuffix);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Tracks an automatically generated index
|
||||
private static abstract class OutputIndexArgumentField extends ArgumentField {
|
||||
protected final String indexFieldName;
|
||||
protected final String originalFieldName;
|
||||
|
|
@ -456,6 +482,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
|
|||
}
|
||||
}
|
||||
|
||||
// Allows setting the format for floats and doubles
|
||||
private static class FormatterArgumentField extends ArgumentField {
|
||||
private final ArgumentField argumentField;
|
||||
public FormatterArgumentField(ArgumentField argumentField) {
|
||||
|
|
|
|||
|
|
@ -121,9 +121,9 @@ public class IndelUtils {
|
|||
boolean done = false;
|
||||
|
||||
ArrayList<Integer> inds = new ArrayList<Integer>();
|
||||
if ( vc.isInsertion() ) {
|
||||
if ( vc.isSimpleInsertion() ) {
|
||||
indelAlleleString = vc.getAlternateAllele(0).getDisplayString();
|
||||
} else if ( vc.isDeletion() ) {
|
||||
} else if ( vc.isSimpleDeletion() ) {
|
||||
indelAlleleString = vc.getReference().getDisplayString();
|
||||
}
|
||||
else {
|
||||
|
|
|
|||
|
|
@ -583,24 +583,24 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
/**
|
||||
* @return true if the alleles indicate a simple insertion (i.e., the reference allele is Null)
|
||||
*/
|
||||
public boolean isInsertion() {
|
||||
// can't just call !isDeletion() because of complex indels
|
||||
return getType() == Type.INDEL && getReference().isNull();
|
||||
public boolean isSimpleInsertion() {
|
||||
// can't just call !isSimpleDeletion() because of complex indels
|
||||
return getType() == Type.INDEL && getReference().isNull() && isBiallelic();
|
||||
}
|
||||
|
||||
/**
|
||||
* @return true if the alleles indicate a simple deletion (i.e., a single alt allele that is Null)
|
||||
*/
|
||||
public boolean isDeletion() {
|
||||
// can't just call !isInsertion() because of complex indels
|
||||
return getType() == Type.INDEL && getAlternateAllele(0).isNull();
|
||||
public boolean isSimpleDeletion() {
|
||||
// can't just call !isSimpleInsertion() because of complex indels
|
||||
return getType() == Type.INDEL && getAlternateAllele(0).isNull() && isBiallelic();
|
||||
}
|
||||
|
||||
/**
|
||||
* @return true if the alleles indicate neither a simple deletion nor a simple insertion
|
||||
*/
|
||||
public boolean isComplexIndel() {
|
||||
return isIndel() && !isDeletion() && !isInsertion();
|
||||
return isIndel() && !isSimpleDeletion() && !isSimpleInsertion();
|
||||
}
|
||||
|
||||
public boolean isSymbolic() {
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("bced1842c78fbabb089dd12b7087050d")
|
||||
Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
|
||||
}
|
||||
|
|
@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("06510bd37ffaa39e817ca0dcaf8f8ac2")
|
||||
Arrays.asList("d470e00a368b5a0468012818994c6a89")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
|
||||
}
|
||||
|
|
@ -72,7 +72,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("19c5b1b6396921c5b1059a2849ae4fcc")
|
||||
Arrays.asList("12856e52c2682328f91594089328596c")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
|
||||
}
|
||||
|
|
@ -93,7 +93,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("a71f8d81cf166cd97ac628092650964a")
|
||||
Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
|
||||
}
|
||||
|
|
@ -114,7 +114,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("4dabe0658232f6174188515db6dfe112")
|
||||
Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
|
||||
}
|
||||
|
|
@ -135,7 +135,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("3340587f10ceff83e5567ddfd1a9a60e")
|
||||
Arrays.asList("15beaf3823c131cabc5fb0445239f978")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
|
||||
}
|
||||
|
|
@ -156,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("c730c7ee31c8138cef6efd8dd04fbbfc")
|
||||
Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
|
||||
}
|
||||
|
|
@ -179,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("2559ca8f454b03e81561f6947f79df18")
|
||||
Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
|
||||
}
|
||||
|
|
@ -204,7 +204,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("23aa5f97641d2fd033095f21c51d2f37")
|
||||
Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
|
||||
}
|
||||
|
|
@ -223,7 +223,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("a69dd3f06903b3f374c6d6f010c653e0")
|
||||
Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
|
||||
}
|
||||
|
|
@ -236,7 +236,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("125fe0a04b5d933cc14016598b2791cd"));
|
||||
1, Arrays.asList("2df4f8911ffc3c8d042298723ed465f8"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -253,7 +253,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ed54aa127b173d8ad8b6482f2a929a42"));
|
||||
executeTestParallel("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
|
|
@ -283,7 +283,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --dbsnp " + b37dbSNP132 +
|
||||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("cbea5f9f8c046d4c014d261db352c43b"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18c44636e36d6657110bf984f8eac181"));
|
||||
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -295,7 +295,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d07a246963ae609643620c839b20cd1e"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1b8ae4fd10de0888bd843f833859d990"));
|
||||
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -373,7 +373,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("44464fe7c89a56cf128a932ef640f7da")
|
||||
Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
|
||||
);
|
||||
executeTest("testAlleleCountStrat", spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -146,8 +146,8 @@ public class VariantContextUnitTest {
|
|||
Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
|
||||
Assert.assertTrue(vc.isSNP());
|
||||
Assert.assertFalse(vc.isIndel());
|
||||
Assert.assertFalse(vc.isInsertion());
|
||||
Assert.assertFalse(vc.isDeletion());
|
||||
Assert.assertFalse(vc.isSimpleInsertion());
|
||||
Assert.assertFalse(vc.isSimpleDeletion());
|
||||
Assert.assertFalse(vc.isMixed());
|
||||
Assert.assertTrue(vc.isBiallelic());
|
||||
Assert.assertEquals(vc.getNAlleles(), 2);
|
||||
|
|
@ -173,8 +173,8 @@ public class VariantContextUnitTest {
|
|||
Assert.assertEquals(VariantContext.Type.NO_VARIATION, vc.getType());
|
||||
Assert.assertFalse(vc.isSNP());
|
||||
Assert.assertFalse(vc.isIndel());
|
||||
Assert.assertFalse(vc.isInsertion());
|
||||
Assert.assertFalse(vc.isDeletion());
|
||||
Assert.assertFalse(vc.isSimpleInsertion());
|
||||
Assert.assertFalse(vc.isSimpleDeletion());
|
||||
Assert.assertFalse(vc.isMixed());
|
||||
Assert.assertFalse(vc.isBiallelic());
|
||||
Assert.assertEquals(vc.getNAlleles(), 1);
|
||||
|
|
@ -199,8 +199,8 @@ public class VariantContextUnitTest {
|
|||
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
|
||||
Assert.assertFalse(vc.isSNP());
|
||||
Assert.assertTrue(vc.isIndel());
|
||||
Assert.assertFalse(vc.isInsertion());
|
||||
Assert.assertTrue(vc.isDeletion());
|
||||
Assert.assertFalse(vc.isSimpleInsertion());
|
||||
Assert.assertTrue(vc.isSimpleDeletion());
|
||||
Assert.assertFalse(vc.isMixed());
|
||||
Assert.assertTrue(vc.isBiallelic());
|
||||
Assert.assertEquals(vc.getNAlleles(), 2);
|
||||
|
|
@ -226,8 +226,8 @@ public class VariantContextUnitTest {
|
|||
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
|
||||
Assert.assertFalse(vc.isSNP());
|
||||
Assert.assertTrue(vc.isIndel());
|
||||
Assert.assertTrue(vc.isInsertion());
|
||||
Assert.assertFalse(vc.isDeletion());
|
||||
Assert.assertTrue(vc.isSimpleInsertion());
|
||||
Assert.assertFalse(vc.isSimpleDeletion());
|
||||
Assert.assertFalse(vc.isMixed());
|
||||
Assert.assertTrue(vc.isBiallelic());
|
||||
Assert.assertEquals(vc.getNAlleles(), 2);
|
||||
|
|
@ -433,7 +433,7 @@ public class VariantContextUnitTest {
|
|||
Assert.assertFalse(vc14.isBiallelic());
|
||||
|
||||
Assert.assertTrue(vc5.isIndel());
|
||||
Assert.assertTrue(vc5.isDeletion());
|
||||
Assert.assertTrue(vc5.isSimpleDeletion());
|
||||
Assert.assertTrue(vc5.isVariant());
|
||||
Assert.assertTrue(vc5.isBiallelic());
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue