Updates to fix some bugs in merger. Now able to merge into project wide indel VCF files. Integration teests coming tomorrow
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3727 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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7be8c35eb2
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b934cc7554
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@ -1,3 +1,27 @@
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broad.tribble.vcf;
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import java.util.Arrays;
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@ -56,6 +80,15 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
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this.lineType = lineType;
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}
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protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType, VCFHeaderVersion version) {
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super(lineType.toString(), "", version);
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this.name = name;
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this.count = count;
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this.type = type;
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this.description = description;
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this.lineType = lineType;
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}
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/**
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* create a VCF format header line
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*
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@ -111,6 +144,12 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
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type == other.type;
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}
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public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {
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return count == other.count &&
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type == other.type &&
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name.equals(other.name);
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}
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/**
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* do we allow flag (boolean) values? (i.e. booleans where you don't have specify the value, AQ means AQ=true)
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* @return true if we do, false otherwise
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@ -1,5 +1,7 @@
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package org.broad.tribble.vcf;
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import org.broadinstitute.sting.utils.Utils;
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import java.util.*;
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@ -35,7 +37,10 @@ public class VCFGenotypeRecord {
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// what kind of phasing this genotype has
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public enum PHASE {
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UNPHASED, PHASED, PHASED_SWITCH_PROB, UNKNOWN
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UNPHASED("/"), PHASED("|"), PHASED_SWITCH_PROB("\\"); // , UNKNOWN
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String genotypeSeparator;
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PHASE(String sep) { this.genotypeSeparator = sep; }
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}
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// our record
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@ -98,14 +103,12 @@ public class VCFGenotypeRecord {
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*/
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static PHASE determinePhase(String phase) {
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// find the phasing information
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if (phase.equals("/"))
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return PHASE.UNPHASED;
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else if (phase.equals("|"))
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return PHASE.PHASED;
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else if (phase.equals("\\"))
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return PHASE.PHASED_SWITCH_PROB;
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else
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throw new IllegalArgumentException("Unknown genotype phasing parameter");
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for ( PHASE p : PHASE.values() ) {
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if (phase.equals(p.genotypeSeparator))
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return p;
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}
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throw new IllegalArgumentException("Unknown genotype phasing parameter: " + phase);
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}
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@ -206,7 +209,7 @@ public class VCFGenotypeRecord {
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}
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public int getPloidy() {
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return 2;
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return mGenotypeAlleles.size();
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}
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public VCFRecord getRecord() {
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@ -214,32 +217,15 @@ public class VCFGenotypeRecord {
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}
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private String toGenotypeString(List<VCFGenotypeEncoding> altAlleles) {
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String str = "";
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boolean first = true;
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List<String> alleleStrings = new ArrayList<String>(altAlleles.size());
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for (VCFGenotypeEncoding allele : mGenotypeAlleles) {
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if (allele.getType() == VCFGenotypeEncoding.TYPE.UNCALLED)
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str += VCFGenotypeRecord.EMPTY_ALLELE;
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alleleStrings.add(VCFGenotypeRecord.EMPTY_ALLELE);
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else
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str += String.valueOf((altAlleles.contains(allele)) ? altAlleles.indexOf(allele) + 1 : 0);
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if (first) {
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switch (mPhaseType) {
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case UNPHASED:
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str += "/";
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break;
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case PHASED:
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str += "|";
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break;
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case PHASED_SWITCH_PROB:
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str += "\\";
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break;
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case UNKNOWN:
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throw new UnsupportedOperationException("Unknown phase type");
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}
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first = false;
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}
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alleleStrings.add(String.valueOf((altAlleles.contains(allele)) ? altAlleles.indexOf(allele) + 1 : 0));
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}
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return str;
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return Utils.join(mPhaseType.genotypeSeparator, alleleStrings);
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}
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@Override
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@ -10,6 +10,10 @@ package org.broad.tribble.vcf;
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*/
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public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
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public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description, VCFHeaderVersion version) {
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super(name, count, type, description, SupportedHeaderLineType.INFO, version);
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}
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public VCFInfoHeaderLine(String name, int count, VCFHeaderLineType type, String description) {
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super(name, count, type, description, SupportedHeaderLineType.INFO);
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}
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@ -23,4 +27,4 @@ public class VCFInfoHeaderLine extends VCFCompoundHeaderLine {
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boolean allowFlagValues() {
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return true;
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}
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}
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}
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@ -136,7 +136,7 @@ public class VCFReaderUtils {
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public static VCFGenotypeRecord getVCFGenotype(String sampleName, String[] keyStrings, String genotypeString, String altAlleles[], char referenceBase) {
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// parameters to create the VCF genotype record
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HashMap<String, String> tagToValue = new HashMap<String, String>();
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VCFGenotypeRecord.PHASE phase = VCFGenotypeRecord.PHASE.UNKNOWN;
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VCFGenotypeRecord.PHASE phase = VCFGenotypeRecord.PHASE.UNPHASED;
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List<VCFGenotypeEncoding> bases = new ArrayList<VCFGenotypeEncoding>();
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for (String key : keyStrings) {
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@ -183,10 +183,10 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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* @param cache
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* @return
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*/
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private static List<Allele> parseGenotypeAlleles(String GT, List<Allele> alleles, Map<String, List<Allele>> cache) {
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private List<Allele> parseGenotypeAlleles(String GT, List<Allele> alleles, Map<String, List<Allele>> cache) {
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// this should cache results [since they are immutable] and return a single object for each genotype
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if ( GT.length() != 3 && GT.length() != 1 )
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throw new StingException("Unreasonable number of alleles: " + "GT=" + GT + " length=" + GT.length()); // 0/1 => barf on 10/0
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throw new VCFParserException("Unreasonable number of alleles: " + "GT=" + GT + " length=" + GT.length()); // 0/1 => barf on 10/0
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List<Allele> GTAlleles = cache.get(GT);
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@ -258,7 +258,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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int count = 0;
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for (String attr : attributes)
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if (Collections.binarySearch(fields,attr) < 0)
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throw new StingException("Unable to find field describing attribute " + attr);
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throw new VCFParserException("Unable to find field describing attribute " + attr);
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}
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}
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@ -282,7 +282,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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List<Allele> alleles = new ArrayList<Allele>(2); // we are almost always biallelic
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// ref
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if (!checkAllele(ref, true))
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throw new StingException("Unable to parse out correct reference allele, we saw = " + ref);
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throw new VCFParserException("Unable to parse out correct reference allele, we saw = " + ref);
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Allele refAllele = Allele.create(ref, true);
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alleles.add(refAllele);
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@ -301,13 +301,13 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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* @param isRef are we the reference allele?
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* @return true if the allele is fine, false otherwise
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*/
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private static boolean checkAllele(String allele,boolean isRef) {
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private boolean checkAllele(String allele,boolean isRef) {
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if (allele.contains("<")) {
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Utils.warnUser("We are currently unable to parse out CNV encodings in VCF, we saw the following allele = " + allele);
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return false;
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}
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else if ( ! Allele.acceptableAlleleBases(allele,isRef) ) {
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throw new StingException("Unparsable vcf record with allele " + allele);
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throw new VCFParserException("Unparsable vcf record with allele " + allele);
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}
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return true;
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}
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@ -320,7 +320,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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*/
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private void parseSingleAllele(List<Allele> alleles, String alt, boolean isRef) {
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if (!checkAllele(alt,isRef))
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throw new StingException("Unable to parse out correct alt allele, we saw = " + alt);
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throw new VCFParserException("Unable to parse out correct alt allele, we saw = " + alt);
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Allele allele = Allele.create(alt, false);
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if ( ! allele.isNoCall() )
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@ -403,10 +403,16 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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}
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return new VariantContext(name, locAndAlleles.first, locAndAlleles.second, genotypes, qual, filters, attributes);
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// } catch ( Exception e ) {
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// // todo -- we need a local exception so that we can remember the location of the throw but also see the line
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// throw new RuntimeException("Line " + lineNo + " generated parser exception " + e.getMessage() + "\nLine: " + Utils.join("\t", parts), e);
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// }
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}
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class VCFParserException extends StingException {
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public VCFParserException(String msg) {
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super("Line " + lineNo + " generated parser exception " + msg);
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}
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public VCFParserException(String msg, Throwable throwable) {
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super("Line " + lineNo + " generated parser exception " + msg, throwable);
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}
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}
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/**
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@ -439,7 +445,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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// check to see if the value list is longer than the key list, which is a problem
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if (nGTKeys < GTValueSplitSize)
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throw new StingException("Too few keys for compared to the value string " + sampleName + ", keys = " + parts[8] + " values = " + parts[genotypeOffset]);
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throw new VCFParserException("Too few keys for compared to the value string " + sampleName + ", keys = " + parts[8] + " values = " + parts[genotypeOffset]);
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int genotypeAlleleLocation = -1;
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if (nGTKeys > 1) {
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@ -449,7 +455,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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gtAttributes.put(genotypeKeyArray[i],".");
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else if (genotypeKeyArray[i].equals("GT"))
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if (i != 0)
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throw new StingException("Saw GT at position " + i + ", it must be at the first position for genotypes. At location = " + locAndAlleles.first);
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throw new VCFParserException("Saw GT at position " + i + ", it must be at the first position for genotypes. At location = " + locAndAlleles.first);
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else
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genotypeAlleleLocation = i;
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else if (genotypeKeyArray[i].equals("GQ"))
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@ -464,7 +470,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
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validateFields(gtAttributes.keySet(), new ArrayList(formatFields.keySet()));
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}
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// check to make sure we found a gentoype field
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if (genotypeAlleleLocation < 0) throw new StingException("Unable to find required field GT for record " + locAndAlleles.first);
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if (genotypeAlleleLocation < 0) throw new VCFParserException("Unable to find required field GT for record " + locAndAlleles.first);
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// assuming allele list length in the single digits, could be bad. Check for > 1 for haploid genotypes
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boolean phased = GTValueArray[genotypeAlleleLocation].length() > 1 && GTValueArray[genotypeAlleleLocation].charAt(1) == '|';
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@ -84,6 +84,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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Set<VCFHeaderLine> headerLines = smartMergeHeaders(vcfRods.values());
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headerLines.add(new VCFHeaderLine("source", "CombineVariants"));
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headerLines.add(new VCFInfoHeaderLine("set", 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants", VCFHeaderVersion.VCF4_0));
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vcfWriter.writeHeader(new VCFHeader(headerLines, samples));
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}
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@ -123,13 +124,18 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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String otherName = ((VCFFilterHeaderLine) other).getName();
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if ( ! lineName.equals(otherName) )
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throw new IllegalStateException("Incompatible header types: " + line + " " + other );
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} else {
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String lineName = ((VCFCompoundHeaderLine) line).getName();
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String otherName = ((VCFCompoundHeaderLine) other).getName();
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} else if ( line instanceof VCFCompoundHeaderLine ) {
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VCFCompoundHeaderLine compLine = (VCFCompoundHeaderLine)line;
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VCFCompoundHeaderLine compOther = (VCFCompoundHeaderLine)other;
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// if the names are the same, but the values are different, we need to quit
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if (lineName.equals(otherName) && !line.equals(other))
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if (! (compLine).equalsExcludingDescription(compOther) )
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throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
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if ( ! compLine.getDescription().equals(compOther) )
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logger.warn(String.format("Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine));
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} else {
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// we are not equal, but we're not anything special either
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logger.warn(String.format("Ignoring header line already in map: this header line = " + line + " already present header = " + other));
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}
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} else {
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map.put(key, line);
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@ -179,4 +185,4 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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if ( vcfWriter != null )
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vcfWriter.close();
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}
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}
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}
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@ -364,11 +364,7 @@ public class VCFWriter {
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continue;
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Object val;
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if (g.hasAttribute(key))
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val = g.getAttribute(key);
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else
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val = new String(MISSING_GENOTYPE_FIELD);
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Object val = g.hasAttribute(key) ? g.getAttribute(key) : MISSING_GENOTYPE_FIELD;
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// some exceptions
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if ( key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ) {
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