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GATKVariantContextUtils.java
1835 lines (1585 loc) · 86 KB
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GATKVariantContextUtils.java
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/*
* Copyright (c) 2012 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.
*/
package org.broadinstitute.sting.utils.variant;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.apache.commons.lang.ArrayUtils;
import org.apache.log4j.Logger;
import org.broad.tribble.TribbleException;
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.vcf.VCFConstants;
import java.io.Serializable;
import java.util.*;
public class GATKVariantContextUtils {
private static Logger logger = Logger.getLogger(GATKVariantContextUtils.class);
public static final int DEFAULT_PLOIDY = 2;
public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
public final static List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
public final static Allele NON_REF_SYMBOLIC_ALLELE = Allele.create("<"+NON_REF_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible non-ref allele at this site
public final static String MERGE_FILTER_PREFIX = "filterIn";
public final static String MERGE_REF_IN_ALL = "ReferenceInAll";
public final static String MERGE_FILTER_IN_ALL = "FilteredInAll";
public final static String MERGE_INTERSECTION = "Intersection";
public enum GenotypeMergeType {
/**
* Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
*/
UNIQUIFY,
/**
* Take genotypes in priority order (see the priority argument).
*/
PRIORITIZE,
/**
* Take the genotypes in any order.
*/
UNSORTED,
/**
* Require that all samples/genotypes be unique between all inputs.
*/
REQUIRE_UNIQUE
}
public enum FilteredRecordMergeType {
/**
* Union - leaves the record if any record is unfiltered.
*/
KEEP_IF_ANY_UNFILTERED,
/**
* Requires all records present at site to be unfiltered. VCF files that don't contain the record don't influence this.
*/
KEEP_IF_ALL_UNFILTERED,
/**
* If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset.
*/
KEEP_UNCONDITIONAL
}
public enum MultipleAllelesMergeType {
/**
* Combine only alleles of the same type (SNP, indel, etc.) into a single VCF record.
*/
BY_TYPE,
/**
* Merge all allele types at the same start position into the same VCF record.
*/
MIX_TYPES
}
/**
* Refactored out of the AverageAltAlleleLength annotation class
* @param vc the variant context
* @return the average length of the alt allele (a double)
*/
public static double getMeanAltAlleleLength(VariantContext vc) {
double averageLength = 1.0;
if ( ! vc.isSNP() && ! vc.isSymbolic() ) {
// adjust for the event length
int averageLengthNum = 0;
int averageLengthDenom = 0;
int refLength = vc.getReference().length();
for ( final Allele a : vc.getAlternateAlleles() ) {
int numAllele = vc.getCalledChrCount(a);
int alleleSize;
if ( a.length() == refLength ) {
// SNP or MNP
byte[] a_bases = a.getBases();
byte[] ref_bases = vc.getReference().getBases();
int n_mismatch = 0;
for ( int idx = 0; idx < a_bases.length; idx++ ) {
if ( a_bases[idx] != ref_bases[idx] )
n_mismatch++;
}
alleleSize = n_mismatch;
}
else if ( a.isSymbolic() ) {
alleleSize = 1;
} else {
alleleSize = Math.abs(refLength-a.length());
}
averageLengthNum += alleleSize*numAllele;
averageLengthDenom += numAllele;
}
averageLength = ( (double) averageLengthNum )/averageLengthDenom;
}
return averageLength;
}
/**
* create a genome location, given a variant context
* @param genomeLocParser parser
* @param vc the variant context
* @return the genomeLoc
*/
public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser,VariantContext vc) {
return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true);
}
public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) {
if (!context.isSNP() || !context.isBiallelic())
throw new IllegalStateException("Requested SNP substitution type for bialleic non-SNP " + context);
return BaseUtils.SNPSubstitutionType(context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]);
}
/**
* If this is a BiAllelic SNP, is it a transition?
*/
public static boolean isTransition(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
/**
* If this is a BiAllelic SNP, is it a transversion?
*/
public static boolean isTransversion(VariantContext context) {
return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
public static boolean isTransition(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION;
}
public static boolean isTransversion(Allele ref, Allele alt) {
return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
}
/**
* Returns a context identical to this with the REF and ALT alleles reverse complemented.
*
* @param vc variant context
* @return new vc
*/
public static VariantContext reverseComplement(VariantContext vc) {
// create a mapping from original allele to reverse complemented allele
HashMap<Allele, Allele> alleleMap = new HashMap<>(vc.getAlleles().size());
for ( final Allele originalAllele : vc.getAlleles() ) {
Allele newAllele;
if ( originalAllele.isNoCall() )
newAllele = originalAllele;
else
newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference());
alleleMap.put(originalAllele, newAllele);
}
// create new Genotype objects
GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) {
List<Allele> newAlleles = new ArrayList<>();
for ( final Allele allele : genotype.getAlleles() ) {
Allele newAllele = alleleMap.get(allele);
if ( newAllele == null )
newAllele = Allele.NO_CALL;
newAlleles.add(newAllele);
}
newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make());
}
return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make();
}
/**
* Returns true iff VC is an non-complex indel where every allele represents an expansion or
* contraction of a series of identical bases in the reference.
*
* For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT
*
* If VC = -/CT, then this function returns true because the CT insertion matches exactly the
* upcoming reference.
* If VC = -/CTA then this function returns false because the CTA isn't a perfect match
*
* Now consider deletions:
*
* If VC = CT/- then again the same logic applies and this returns true
* The case of CTA/- makes no sense because it doesn't actually match the reference bases.
*
* The logic of this function is pretty simple. Take all of the non-null alleles in VC. For
* each insertion allele of n bases, check if that allele matches the next n reference bases.
* For each deletion allele of n bases, check if this matches the reference bases at n - 2 n,
* as it must necessarily match the first n bases. If this test returns true for all
* alleles you are a tandem repeat, otherwise you are not.
*
* @param vc
* @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference
* @return
*/
@Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
if ( ! vc.isIndel() ) // only indels are tandem repeats
return false;
final Allele ref = vc.getReference();
for ( final Allele allele : vc.getAlternateAlleles() ) {
if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) )
return false;
}
// we've passed all of the tests, so we are a repeat
return true;
}
/**
*
* @param vc
* @param refBasesStartingAtVCWithPad
* @return
*/
@Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
public static Pair<List<Integer>,byte[]> getNumTandemRepeatUnits(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
final boolean VERBOSE = false;
final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
if ( ! vc.isIndel() ) // only indels are tandem repeats
return null;
final Allele refAllele = vc.getReference();
final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length());
byte[] repeatUnit = null;
final ArrayList<Integer> lengths = new ArrayList<>();
for ( final Allele allele : vc.getAlternateAlleles() ) {
Pair<int[],byte[]> result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes());
final int[] repetitionCount = result.first;
// repetition count = 0 means allele is not a tandem expansion of context
if (repetitionCount[0] == 0 || repetitionCount[1] == 0)
return null;
if (lengths.size() == 0) {
lengths.add(repetitionCount[0]); // add ref allele length only once
}
lengths.add(repetitionCount[1]); // add this alt allele's length
repeatUnit = result.second;
if (VERBOSE) {
System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad);
System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0]));
System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1]));
System.out.println("RU:"+new String(repeatUnit));
}
}
return new Pair<List<Integer>, byte[]>(lengths,repeatUnit);
}
public static Pair<int[],byte[]> getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) {
/* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units.
Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)2.
*/
byte[] longB;
// find first repeat unit based on either ref or alt, whichever is longer
if (altBases.length > refBases.length)
longB = altBases;
else
longB = refBases;
// see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units
// for example, -*,CACA needs to first be decomposed into (CA)2
final int repeatUnitLength = findRepeatedSubstring(longB);
final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength);
final int[] repetitionCount = new int[2];
// look for repetitions forward on the ref bases (i.e. starting at beginning of ref bases)
int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases, true);
repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext), true)-repetitionsInRef;
repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext), true)-repetitionsInRef;
return new Pair<>(repetitionCount, repeatUnit);
}
/**
* Find out if a string can be represented as a tandem number of substrings.
* For example ACTACT is a 2-tandem of ACT,
* but ACTACA is not.
*
* @param bases String to be tested
* @return Length of repeat unit, if string can be represented as tandem of substring (if it can't
* be represented as one, it will be just the length of the input string)
*/
public static int findRepeatedSubstring(byte[] bases) {
int repLength;
for (repLength=1; repLength <=bases.length; repLength++) {
final byte[] candidateRepeatUnit = Arrays.copyOf(bases,repLength);
boolean allBasesMatch = true;
for (int start = repLength; start < bases.length; start += repLength ) {
// check that remaining of string is exactly equal to repeat unit
final byte[] basePiece = Arrays.copyOfRange(bases,start,start+candidateRepeatUnit.length);
if (!Arrays.equals(candidateRepeatUnit, basePiece)) {
allBasesMatch = false;
break;
}
}
if (allBasesMatch)
return repLength;
}
return repLength;
}
/**
* Helper routine that finds number of repetitions a string consists of.
* For example, for string ATAT and repeat unit AT, number of repetitions = 2
* @param repeatUnit Substring
* @param testString String to test
* @oaram lookForward Look for repetitions forward (at beginning of string) or backward (at end of string)
* @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
*/
public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString, boolean lookForward) {
int numRepeats = 0;
if (lookForward) {
// look forward on the test string
for (int start = 0; start < testString.length; start += repeatUnit.length) {
int end = start + repeatUnit.length;
byte[] unit = Arrays.copyOfRange(testString,start, end);
if(Arrays.equals(unit,repeatUnit))
numRepeats++;
else
break;
}
return numRepeats;
}
// look backward. For example, if repeatUnit = AT and testString = GATAT, number of repeat units is still 2
// look forward on the test string
for (int start = testString.length - repeatUnit.length; start >= 0; start -= repeatUnit.length) {
int end = start + repeatUnit.length;
byte[] unit = Arrays.copyOfRange(testString,start, end);
if(Arrays.equals(unit,repeatUnit))
numRepeats++;
else
break;
}
return numRepeats;
}
/**
* Helper function for isTandemRepeat that checks that allele matches somewhere on the reference
* @param ref
* @param alt
* @param refBasesStartingAtVCWithoutPad
* @return
*/
protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) {
if ( ! Allele.oneIsPrefixOfOther(ref, alt) )
return false; // we require one allele be a prefix of another
if ( ref.length() > alt.length() ) { // we are a deletion
return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2);
} else { // we are an insertion
return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1);
}
}
protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) {
final String potentialRepeat = l.substring(s.length()); // skip s bases
for ( int i = 0; i < minNumberOfMatches; i++) {
final int start = i * potentialRepeat.length();
final int end = (i+1) * potentialRepeat.length();
if ( ref.length() < end )
return false; // we ran out of bases to test
final String refSub = ref.substring(start, end);
if ( ! refSub.equals(potentialRepeat) )
return false; // repeat didn't match, fail
}
return true; // we passed all tests, we matched
}
public enum GenotypeAssignmentMethod {
/**
* set all of the genotype GT values to NO_CALL
*/
SET_TO_NO_CALL,
/**
* Use the subsetted PLs to greedily assigned genotypes
*/
USE_PLS_TO_ASSIGN,
/**
* Try to match the original GT calls, if at all possible
*
* Suppose I have 3 alleles: A/B/C and the following samples:
*
* original_GT best_match to A/B best_match to A/C
* S1 => A/A A/A A/A
* S2 => A/B A/B A/A
* S3 => B/B B/B A/A
* S4 => B/C A/B A/C
* S5 => C/C A/A C/C
*
* Basically, all alleles not in the subset map to ref. It means that het-alt genotypes
* when split into 2 bi-allelic variants will be het in each, which is good in some cases,
* rather than the undetermined behavior when using the PLs to assign, which could result
* in hom-var or hom-ref for each, depending on the exact PL values.
*/
BEST_MATCH_TO_ORIGINAL,
/**
* do not even bother changing the GTs
*/
DO_NOT_ASSIGN_GENOTYPES
}
/**
* subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
*
* @param vc variant context with genotype likelihoods
* @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
* @param assignGenotypes assignment strategy for the (subsetted) PLs
* @return a new non-null GenotypesContext
*/
public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
final List<Allele> allelesToUse,
final GenotypeAssignmentMethod assignGenotypes) {
if ( allelesToUse.get(0).isNonReference() ) throw new IllegalArgumentException("First allele must be the reference allele");
if ( allelesToUse.size() == 1 ) throw new IllegalArgumentException("Cannot subset to only 1 alt allele");
// optimization: if no input genotypes, just exit
if (vc.getGenotypes().isEmpty()) return GenotypesContext.create();
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
final List<Integer> likelihoodIndexesToUse = determineLikelihoodIndexesToUse(vc, allelesToUse);
// create the new genotypes
return createGenotypesWithSubsettedLikelihoods(vc.getGenotypes(), vc, allelesToUse, likelihoodIndexesToUse, assignGenotypes);
}
/**
* Figure out which likelihood indexes to use for a selected down set of alleles
*
* @param originalVC the original VariantContext
* @param allelesToUse the subset of alleles to use
* @return a list of PL indexes to use or null if none
*/
private static List<Integer> determineLikelihoodIndexesToUse(final VariantContext originalVC, final List<Allele> allelesToUse) {
// the bitset representing the allele indexes we want to keep
final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);
// an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
// then we can keep the PLs as is; otherwise, we determine which ones to keep
if ( MathUtils.countOccurrences(true, alleleIndexesToUse) == alleleIndexesToUse.length )
return null;
return getLikelihoodIndexes(originalVC, alleleIndexesToUse);
}
/**
* Get the actual likelihoods indexes to use given the corresponding allele indexes
*
* @param originalVC the original VariantContext
* @param alleleIndexesToUse the bitset representing the alleles to use (@see #getAlleleIndexBitset)
* @return a non-null List
*/
private static List<Integer> getLikelihoodIndexes(final VariantContext originalVC, final boolean[] alleleIndexesToUse) {
final List<Integer> result = new ArrayList<>(30);
// numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(originalVC.getNAlleles(), DEFAULT_PLOIDY);
for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
// consider this entry only if both of the alleles are good
if ( alleleIndexesToUse[alleles.alleleIndex1] && alleleIndexesToUse[alleles.alleleIndex2] )
result.add(PLindex);
}
return result;
}
/**
* Given an original VariantContext and a list of alleles from that VC to keep,
* returns a bitset representing which allele indexes should be kept
*
* @param originalVC the original VC
* @param allelesToKeep the list of alleles to keep
* @return non-null bitset
*/
private static boolean[] getAlleleIndexBitset(final VariantContext originalVC, final List<Allele> allelesToKeep) {
final int numOriginalAltAlleles = originalVC.getNAlleles() - 1;
final boolean[] alleleIndexesToKeep = new boolean[numOriginalAltAlleles + 1];
// the reference Allele is definitely still used
alleleIndexesToKeep[0] = true;
for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
if ( allelesToKeep.contains(originalVC.getAlternateAllele(i)) )
alleleIndexesToKeep[i+1] = true;
}
return alleleIndexesToKeep;
}
/**
* Create the new GenotypesContext with the subsetted PLs
*
* @param originalGs the original GenotypesContext
* @param vc the original VariantContext
* @param allelesToUse the actual alleles to use with the new Genotypes
* @param likelihoodIndexesToUse the indexes in the PL to use given the allelesToUse (@see #determineLikelihoodIndexesToUse())
* @param assignGenotypes assignment strategy for the (subsetted) PLs
* @return a new non-null GenotypesContext
*/
private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final GenotypesContext originalGs,
final VariantContext vc,
final List<Allele> allelesToUse,
final List<Integer> likelihoodIndexesToUse,
final GenotypeAssignmentMethod assignGenotypes) {
// the new genotypes to create
final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());
// make sure we are seeing the expected number of likelihoods per sample
final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);
// the samples
final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();
// create the new genotypes
for ( int k = 0; k < originalGs.size(); k++ ) {
final Genotype g = originalGs.get(sampleIndices.get(k));
final GenotypeBuilder gb = new GenotypeBuilder(g);
// create the new likelihoods array from the alleles we are allowed to use
double[] newLikelihoods;
if ( !g.hasLikelihoods() ) {
// we don't have any likelihoods, so we null out PLs and make G ./.
newLikelihoods = null;
gb.noPL();
} else {
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
if ( likelihoodIndexesToUse == null ) {
newLikelihoods = originalLikelihoods;
} else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
logger.warn("Wrong number of likelihoods in sample " + g.getSampleName() + " at " + vc + " got " + g.getLikelihoodsString() + " but expected " + expectedNumLikelihoods);
newLikelihoods = null;
} else {
newLikelihoods = new double[likelihoodIndexesToUse.size()];
int newIndex = 0;
for ( final int oldIndex : likelihoodIndexesToUse )
newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
// might need to re-normalize
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
}
if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) )
gb.noPL();
else
gb.PL(newLikelihoods);
}
updateGenotypeAfterSubsetting(g.getAlleles(), gb, assignGenotypes, newLikelihoods, allelesToUse);
newGTs.add(gb.make());
}
return newGTs;
}
private static boolean likelihoodsAreUninformative(final double[] likelihoods) {
return MathUtils.sum(likelihoods) > SUM_GL_THRESH_NOCALL;
}
/**
* Add the genotype call (GT) field to GenotypeBuilder using the requested algorithm assignmentMethod
*
* @param originalGT the original genotype calls, cannot be null
* @param gb the builder where we should put our newly called alleles, cannot be null
* @param assignmentMethod the method to use to do the assignment, cannot be null
* @param newLikelihoods a vector of likelihoods to use if the method requires PLs, should be log10 likelihoods, cannot be null
* @param allelesToUse the alleles we are using for our subsetting
*/
public static void updateGenotypeAfterSubsetting(final List<Allele> originalGT,
final GenotypeBuilder gb,
final GenotypeAssignmentMethod assignmentMethod,
final double[] newLikelihoods,
final List<Allele> allelesToUse) {
switch ( assignmentMethod ) {
case DO_NOT_ASSIGN_GENOTYPES:
break;
case SET_TO_NO_CALL:
gb.alleles(NO_CALL_ALLELES);
gb.noAD();
gb.noGQ();
break;
case USE_PLS_TO_ASSIGN:
gb.noAD();
if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) ) {
// if there is no mass on the (new) likelihoods, then just no-call the sample
gb.alleles(NO_CALL_ALLELES);
gb.noGQ();
} else {
// find the genotype with maximum likelihoods
final int PLindex = MathUtils.maxElementIndex(newLikelihoods);
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
gb.alleles(Arrays.asList(allelesToUse.get(alleles.alleleIndex1), allelesToUse.get(alleles.alleleIndex2)));
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
}
break;
case BEST_MATCH_TO_ORIGINAL:
final List<Allele> best = new LinkedList<>();
final Allele ref = allelesToUse.get(0); // WARNING -- should be checked in input argument
for ( final Allele originalAllele : originalGT ) {
best.add(allelesToUse.contains(originalAllele) ? originalAllele : ref);
}
gb.noGQ();
gb.noPL();
gb.noAD();
gb.alleles(best);
break;
}
}
/**
* Subset the samples in VC to reference only information with ref call alleles
*
* Preserves DP if present
*
* @param vc the variant context to subset down to
* @param ploidy ploidy to use if a genotype doesn't have any alleles
* @return a GenotypesContext
*/
public static GenotypesContext subsetToRefOnly(final VariantContext vc, final int ploidy) {
if ( vc == null ) throw new IllegalArgumentException("vc cannot be null");
if ( ploidy < 1 ) throw new IllegalArgumentException("ploidy must be >= 1 but got " + ploidy);
// the genotypes with PLs
final GenotypesContext oldGTs = vc.getGenotypes();
// optimization: if no input genotypes, just exit
if (oldGTs.isEmpty()) return oldGTs;
// the new genotypes to create
final GenotypesContext newGTs = GenotypesContext.create(oldGTs.size());
final Allele ref = vc.getReference();
final List<Allele> diploidRefAlleles = Arrays.asList(ref, ref);
// create the new genotypes
for ( final Genotype g : vc.getGenotypes() ) {
final int gPloidy = g.getPloidy() == 0 ? ploidy : g.getPloidy();
final List<Allele> refAlleles = gPloidy == 2 ? diploidRefAlleles : Collections.nCopies(gPloidy, ref);
final GenotypeBuilder gb = new GenotypeBuilder(g.getSampleName(), refAlleles);
if ( g.hasDP() ) gb.DP(g.getDP());
if ( g.hasGQ() ) gb.GQ(g.getGQ());
newGTs.add(gb.make());
}
return newGTs;
}
/**
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
*
* @param vc variant context with genotype likelihoods
* @return genotypes context
*/
public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) {
return subsetDiploidAlleles(vc, vc.getAlleles(), GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN);
}
/**
* Split variant context into its biallelic components if there are more than 2 alleles
*
* For VC has A/B/C alleles, returns A/B and A/C contexts.
* Genotypes are all no-calls now (it's not possible to fix them easily)
* Alleles are right trimmed to satisfy VCF conventions
*
* If vc is biallelic or non-variant it is just returned
*
* Chromosome counts are updated (but they are by definition 0)
*
* @param vc a potentially multi-allelic variant context
* @return a list of bi-allelic (or monomorphic) variant context
*/
public static List<VariantContext> splitVariantContextToBiallelics(final VariantContext vc) {
return splitVariantContextToBiallelics(vc, false, GenotypeAssignmentMethod.SET_TO_NO_CALL);
}
/**
* Split variant context into its biallelic components if there are more than 2 alleles
*
* For VC has A/B/C alleles, returns A/B and A/C contexts.
* Genotypes are all no-calls now (it's not possible to fix them easily)
* Alleles are right trimmed to satisfy VCF conventions
*
* If vc is biallelic or non-variant it is just returned
*
* Chromosome counts are updated (but they are by definition 0)
*
* @param vc a potentially multi-allelic variant context
* @param trimLeft if true, we will also left trim alleles, potentially moving the resulting vcs forward on the genome
* @return a list of bi-allelic (or monomorphic) variant context
*/
public static List<VariantContext> splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod) {
if ( ! vc.isVariant() || vc.isBiallelic() )
// non variant or biallelics already satisfy the contract
return Collections.singletonList(vc);
else {
final List<VariantContext> biallelics = new LinkedList<>();
for ( final Allele alt : vc.getAlternateAlleles() ) {
VariantContextBuilder builder = new VariantContextBuilder(vc);
final List<Allele> alleles = Arrays.asList(vc.getReference(), alt);
builder.alleles(alleles);
builder.genotypes(subsetDiploidAlleles(vc, alleles, genotypeAssignmentMethod));
VariantContextUtils.calculateChromosomeCounts(builder, true);
final VariantContext trimmed = trimAlleles(builder.make(), trimLeft, true);
biallelics.add(trimmed);
}
return biallelics;
}
}
public static Genotype removePLsAndAD(final Genotype g) {
return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g;
}
/**
* Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided.
* If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
* the sample name
*
* @param unsortedVCs collection of unsorted VCs
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
* @param genotypeMergeOptions merge option for genotypes
* @param annotateOrigin should we annotate the set it came from?
* @param printMessages should we print messages?
* @param setKey the key name of the set
* @param filteredAreUncalled are filtered records uncalled?
* @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count?
* @param combineAnnotations should we merge info field annotations by assuming the incoming VCs are i.i.d.
* @return new VariantContext representing the merge of unsortedVCs
*/
public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
final List<String> priorityListOfVCs,
final FilteredRecordMergeType filteredRecordMergeType,
final GenotypeMergeType genotypeMergeOptions,
final boolean annotateOrigin,
final boolean printMessages,
final String setKey,
final boolean filteredAreUncalled,
final boolean mergeInfoWithMaxAC,
final boolean combineAnnotations ) {
int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size();
return simpleMerge(unsortedVCs, Collections.<VariantContext>emptyList(), priorityListOfVCs, originalNumOfVCs, filteredRecordMergeType, genotypeMergeOptions, annotateOrigin, printMessages, setKey, filteredAreUncalled, mergeInfoWithMaxAC, combineAnnotations);
}
/**
* Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided.
* If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
* the sample name.
* simpleMerge does not verify any more unique sample names EVEN if genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE. One should use
* SampleUtils.verifyUniqueSamplesNames to check that before using simpleMerge.
*
* For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/
*
* @param unsortedVCs collection of unsorted VCs
* @param potentialRefVCs collection of unsorted VCs that overlap this locus which should only be searched for potential reference records
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
* @param genotypeMergeOptions merge option for genotypes
* @param annotateOrigin should we annotate the set it came from?
* @param printMessages should we print messages?
* @param setKey the key name of the set
* @param filteredAreUncalled are filtered records uncalled?
* @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count?
* @param combineAnnotations should we merge info field annotations by assuming the incoming VCs are i.i.d.
* @return new VariantContext representing the merge of unsortedVCs
*/
public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
final Collection<VariantContext> potentialRefVCs,
final List<String> priorityListOfVCs,
final int originalNumOfVCs,
final FilteredRecordMergeType filteredRecordMergeType,
final GenotypeMergeType genotypeMergeOptions,
final boolean annotateOrigin,
final boolean printMessages,
final String setKey,
final boolean filteredAreUncalled,
final boolean mergeInfoWithMaxAC,
final boolean combineAnnotations ) {
if ( unsortedVCs == null || unsortedVCs.size() == 0 )
return null;
if (priorityListOfVCs != null && originalNumOfVCs != priorityListOfVCs.size())
throw new IllegalArgumentException("the number of the original VariantContexts must be the same as the number of VariantContexts in the priority list");
if ( annotateOrigin && priorityListOfVCs == null && originalNumOfVCs == 0)
throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts or the number of original VariantContexts");
final List<VariantContext> preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions);
// Make sure all variant contexts are padded with reference base in case of indels if necessary
List<VariantContext> VCs = new ArrayList<>();
for (final VariantContext vc : preFilteredVCs) {
if ( ! filteredAreUncalled || vc.isNotFiltered() )
VCs.add(vc);
}
// cycle through and fill in NON_REF_SYMBOLIC_ALLELEs with the actual alternate allele if possible
VCs = fillInNonRefSymbolicAlleles(VCs, potentialRefVCs);
if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled
return null;
// establish the baseline info from the first VC
final VariantContext first = VCs.get(0);
final String name = first.getSource();
final Allele refAllele = determineReferenceAllele(VCs);
final Set<Allele> alleles = new LinkedHashSet<>();
final Set<String> filters = new HashSet<>();
final Map<String, Object> attributes = new LinkedHashMap<>();
final Set<String> inconsistentAttributes = new HashSet<>();
final Set<String> variantSources = new HashSet<>(); // contains the set of sources we found in our set of VCs that are variant
final Set<String> rsIDs = new LinkedHashSet<>(1); // most of the time there's one id
VariantContext longestVC = first;
int depth = 0;
int maxAC = -1;
final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<>();
final Map<String, List<Comparable>> annotationMap = new LinkedHashMap<>();
double log10PError = CommonInfo.NO_LOG10_PERROR;
boolean anyVCHadFiltersApplied = false;
VariantContext vcWithMaxAC = null;
GenotypesContext genotypes = GenotypesContext.create();
// counting the number of filtered and variant VCs
int nFiltered = 0;
boolean remapped = false;
// cycle through and add info from the other VCs, making sure the loc/reference matches
for ( final VariantContext vc : VCs ) {
if ( longestVC.getStart() != vc.getStart() )
throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
if ( VariantContextUtils.getSize(vc) > VariantContextUtils.getSize(longestVC) )
longestVC = vc; // get the longest location
nFiltered += vc.isFiltered() ? 1 : 0;
if ( vc.isVariant() ) variantSources.add(vc.getSource());
AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles);
remapped = remapped || alleleMapping.needsRemapping();
alleles.addAll(alleleMapping.values());
mergeGenotypes(genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY);
// We always take the QUAL of the first VC with a non-MISSING qual for the combined value
if ( log10PError == CommonInfo.NO_LOG10_PERROR )
log10PError = vc.getLog10PError();
filters.addAll(vc.getFilters());
anyVCHadFiltersApplied |= vc.filtersWereApplied();
//
// add attributes
//
// special case DP (add it up) and ID (just preserve it)
//
if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
if ( vc.hasID() ) rsIDs.add(vc.getID());
if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
// lets see if the string contains a "," separator
if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) {
final List<String> alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
for (final String alleleCount : alleleCountArray) {
final int ac = Integer.valueOf(alleleCount.trim());
if (ac > maxAC) {
maxAC = ac;
vcWithMaxAC = vc;
}
}
} else {
final int ac = Integer.valueOf(rawAlleleCounts);
if (ac > maxAC) {
maxAC = ac;
vcWithMaxAC = vc;
}
}
}
for (final Map.Entry<String, Object> p : vc.getAttributes().entrySet()) {
final String key = p.getKey();
final Object value = p.getValue();
boolean badAnnotation = false;
if ( combineAnnotations ) { // add the annotation values to a list for combining later
List<Comparable> values = annotationMap.get(key);
if( values == null ) {
values = new ArrayList<>();
annotationMap.put(key, values);
}
try {
final String stringValue = value.toString();
// Branch to avoid unintentional, implicit type conversions that occur with the ? operator.
if (stringValue.contains("."))
values.add(Double.parseDouble(stringValue));
else
values.add(Integer.parseInt(stringValue));
} catch (NumberFormatException e) {
badAnnotation = true;
}
}
if ( ! combineAnnotations || badAnnotation ) { // only output annotations that have the same value in every input VC
// if we don't like the key already, don't go anywhere
if ( ! inconsistentAttributes.contains(key) ) {
final boolean alreadyFound = attributes.containsKey(key);
final Object boundValue = attributes.get(key);
final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);
if ( alreadyFound && ! boundValue.equals(value) && ! boundIsMissingValue ) {
// we found the value but we're inconsistent, put it in the exclude list
inconsistentAttributes.add(key);
attributes.remove(key);
} else if ( ! alreadyFound || boundIsMissingValue ) { // no value
attributes.put(key, value);
}
}
}
}
}
// if we have more alternate alleles in the merged VC than in one or more of the
// original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF, and AD
for ( final VariantContext vc : VCs ) {
if (vc.getAlleles().size() == 1)
continue;
if ( hasPLIncompatibleAlleles(alleles, vc.getAlleles())) {
if ( ! genotypes.isEmpty() ) {
logger.debug(String.format("Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s",
vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.getAlleles()));
}
genotypes = stripPLsAndAD(genotypes);