More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF:
- Fixed and cleaned code to produce trailing and padding bases in alleles around indels. - Deal better with missing fields. Pending: - Chopping missing fields at end of genotypes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3679 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel
parent
12c0de6170
commit
d932322190
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@ -4,9 +4,9 @@ import java.util.*;
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/**
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*
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* @author aaron
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*
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*
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* @author aaron
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*
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* Class VCFGenotypeRecord
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*
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* A descriptions should go here. Blame aaron if it's missing.
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@ -201,8 +201,8 @@ public class VCFGenotypeRecord {
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public boolean isFiltered() {
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return ( mFields.get(GENOTYPE_FILTER_KEY) != null &&
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!mFields.get(GENOTYPE_FILTER_KEY).equals(UNFILTERED) &&
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!mFields.get(GENOTYPE_FILTER_KEY).equals(PASSES_FILTERS));
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!mFields.get(GENOTYPE_FILTER_KEY).equals(UNFILTERED) &&
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!mFields.get(GENOTYPE_FILTER_KEY).equals(PASSES_FILTERS));
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}
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public int getPloidy() {
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@ -275,6 +275,10 @@ public class VCFGenotypeRecord {
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* @return a string
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*/
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public String toStringEncoding(List<VCFGenotypeEncoding> altAlleles, String[] genotypeFormatStrings) {
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return toStringEncoding(altAlleles, genotypeFormatStrings, false);
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}
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public String toStringEncoding(List<VCFGenotypeEncoding> altAlleles, String[] genotypeFormatStrings, boolean doVCF40) {
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StringBuilder builder = new StringBuilder();
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builder.append(toGenotypeString(altAlleles));
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@ -288,7 +292,7 @@ public class VCFGenotypeRecord {
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builder.append(VCFRecord.GENOTYPE_FIELD_SEPERATOR);
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if ( value == null || value.equals("") )
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builder.append(getMissingFieldValue(field));
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builder.append(getMissingFieldValue(field, doVCF40));
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else
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builder.append(value);
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}
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@ -304,6 +308,10 @@ public class VCFGenotypeRecord {
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* @return a string
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*/
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public static String stringEncodingForEmptyGenotype(String[] genotypeFormatStrings) {
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// backward compatibility to VCF 3.3
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return stringEncodingForEmptyGenotype(genotypeFormatStrings, false);
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}
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public static String stringEncodingForEmptyGenotype(String[] genotypeFormatStrings, boolean doVCF40) {
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StringBuilder builder = new StringBuilder();
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builder.append(EMPTY_GENOTYPE);
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@ -311,26 +319,47 @@ public class VCFGenotypeRecord {
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if ( field.equals(GENOTYPE_KEY) )
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continue;
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builder.append(VCFRecord.GENOTYPE_FIELD_SEPERATOR);
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builder.append(getMissingFieldValue(field));
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// in VCF4.0, if a genotype is empty only the ./. key can be included
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if (!doVCF40) {
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builder.append(VCFRecord.GENOTYPE_FIELD_SEPERATOR);
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builder.append(getMissingFieldValue(field));
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}
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}
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return builder.toString();
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}
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public static String getMissingFieldValue(String field) {
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String result = "";
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if ( field.equals(GENOTYPE_QUALITY_KEY) )
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result = String.valueOf(MISSING_GENOTYPE_QUALITY);
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else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) )
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result = String.valueOf(MISSING_DEPTH);
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else if ( field.equals(GENOTYPE_FILTER_KEY) )
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result = UNFILTERED;
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else if ( field.equals(GENOTYPE_LIKELIHOODS_KEY) )
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result = "0,0,0";
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// TODO -- support haplotype quality
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//else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
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// result = String.valueOf(MISSING_HAPLOTYPE_QUALITY);
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// backward compatibility to VCF 3.3
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return getMissingFieldValue(field, false);
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}
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public static String getMissingFieldValue(String field, boolean doVCF40) {
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String result;
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if (doVCF40) {
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result = "."; // default missing value
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// TODO - take number of elements in field as input and output corresponding .'s
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if ( field.equals(GENOTYPE_LIKELIHOODS_KEY) )
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result = ".,.,.";
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else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
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result = ".,.";
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}
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else {
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result = "";
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if ( field.equals(GENOTYPE_QUALITY_KEY) )
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result = String.valueOf(MISSING_GENOTYPE_QUALITY);
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else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) )
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result = String.valueOf(MISSING_DEPTH);
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else if ( field.equals(GENOTYPE_FILTER_KEY) )
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result = UNFILTERED;
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else if ( field.equals(GENOTYPE_LIKELIHOODS_KEY) )
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result = "0,0,0";
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// TODO -- support haplotype quality
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//else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
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// result = String.valueOf(MISSING_HAPLOTYPE_QUALITY);
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}
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return result;
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}
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@ -143,10 +143,13 @@ public class VCFWriter {
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// write out the column line
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StringBuilder b = new StringBuilder();
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b.append(VCFHeader.HEADER_INDICATOR);
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for (VCFHeader.HEADER_FIELDS field : header.getHeaderFields()) b.append(field + FIELD_SEPARATOR);
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for (VCFHeader.HEADER_FIELDS field : header.getHeaderFields())
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b.append(field + FIELD_SEPARATOR);
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if (header.hasGenotypingData()) {
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b.append("FORMAT" + FIELD_SEPARATOR);
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for (String field : header.getGenotypeSamples()) b.append(field + FIELD_SEPARATOR);
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for (String field : header.getGenotypeSamples())
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b.append(field + FIELD_SEPARATOR);
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}
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mWriter.write(b.toString() + "\n");
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mWriter.flush(); // necessary so that writing to an output stream will work
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@ -224,15 +227,9 @@ public class VCFWriter {
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long position = loc.getStart();
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String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : EMPTY_ID_FIELD;
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builder.append(contig);
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builder.append(FIELD_SEPARATOR);
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builder.append(position);
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builder.append(FIELD_SEPARATOR);
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builder.append(ID);
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builder.append(FIELD_SEPARATOR);
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// deal with the reference
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String referenceBases = new String(vc.getReference().getBases());
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String referenceFromVC = new String(vc.getReference().getBases());
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double qual = vc.hasNegLog10PError() ? vc.getPhredScaledQual() : -1;
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// TODO- clean up these flags and associated code
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@ -241,7 +238,6 @@ public class VCFWriter {
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boolean filtersWereAppliedToGenotypes = false;
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String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? PASSES_FILTERS_VCF_4_0 : UNFILTERED);
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String referenceString = new String(vc.getReference().getBases());
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Map<Allele, VCFGenotypeEncoding> alleleMap = new HashMap<Allele, VCFGenotypeEncoding>();
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alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
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List<VCFGenotypeEncoding> vcfAltAlleles = new ArrayList<VCFGenotypeEncoding>();
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@ -252,12 +248,7 @@ public class VCFWriter {
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ArrayList<Allele> originalAlleles = (ArrayList)vc.getAttribute("ORIGINAL_ALLELE_LIST");
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boolean isComplexEvent = false;
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if (referenceBases.length()>1) {
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// complex event: by VCF 4.0, reference from previous position is included.
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position--;
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isComplexEvent = true;
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}
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// search for reference allele and find trailing and padding at the end.
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if (originalAlleles != null) {
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@ -277,7 +268,16 @@ public class VCFWriter {
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String refString = new String(a.getBases());
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String originalRef = new String(originalReferenceAllele.getBases());
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numTrailingBases = originalRef.indexOf(refString);
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if (refString.equals("")) {
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// special case with null reference:
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// for example, null reference, originalRef = "AC", alt = "AGC".
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// In this case, we'd have one trailing and one padding base, with alleles as {-,G}.
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// TEMP fix: assume in this case one trailing base, more general solution would be to
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// scan through all alleles and look for maximum common subsequence at beginning and at end for all alleles
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numTrailingBases = 1;
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} else
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numTrailingBases = originalRef.indexOf(refString);
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numPaddingBases = originalRef.length()-refString.length()-numTrailingBases;
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if (numTrailingBases > 0) {
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@ -285,57 +285,32 @@ public class VCFWriter {
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trailingBases = originalRef.substring(0,numTrailingBases);
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}
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if (numPaddingBases > 0)
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paddingBases = originalRef.substring(refString.length(),originalRef.length()-1);
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paddingBases = originalRef.substring(originalRef.length()-numPaddingBases,originalRef.length());
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}
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} else {
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// no original Allele information:
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if (isComplexEvent)
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position--;
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// no original Allele information: add one common base to all alleles (reference at this location)
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trailingBases = new String(refBases);
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numTrailingBases = 1;
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position--;
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}
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for ( Allele a : vc.getAlleles() ) {
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VCFGenotypeEncoding encoding;
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String alleleString = new String(a.getBases());
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if ( isComplexEvent ) {
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// Mixed variants (e.g. microsatellites) have the reference before the event included
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String s;
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if (numTrailingBases > 0) {
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s = trailingBases+alleleString+paddingBases;
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} else {
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s = new String(refBases)+alleleString;
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}
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encoding = new VCFGenotypeEncoding(s, true);
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if (a.isReference())
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referenceString = s;
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String s = trailingBases+alleleString+paddingBases;
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encoding = new VCFGenotypeEncoding(s, true);
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} else if ( vc.getType() == VariantContext.Type.INDEL ) {
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if ( a.isNull() ) {
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if ( a.isReference() ) {
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// ref, where alt is insertion
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encoding = new VCFGenotypeEncoding(new String(refBases));
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} else {
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// non-ref deletion
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encoding = new VCFGenotypeEncoding(".");
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}
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} else if ( a.isReference() ) {
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// ref, where alt is deletion
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encoding = new VCFGenotypeEncoding(new String(refBases));
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} else {
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// non-ref insertion
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referenceString = new String(refBases)+alleleString;
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encoding = new VCFGenotypeEncoding(referenceString, true);
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}
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} else {
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// no variation, ref or alt for snp
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encoding = new VCFGenotypeEncoding(alleleString);
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}
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// overwrite reference string by possibly padded version
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if (a.isReference())
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referenceFromVC = s;
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if ( a.isNonReference() ) {
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else {
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vcfAltAlleles.add(encoding);
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}
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@ -375,8 +350,11 @@ public class VCFWriter {
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if ( key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ) {
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if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 )
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val = VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY;
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else
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val = Math.min(g.getPhredScaledQual(), VCFGenotypeRecord.MAX_QUAL_VALUE);
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else {
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// TODO - check whether we need to saturate quality to 99 as in VCF3.3 coder. For now allow unbounded values
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// val = Math.min(g.getPhredScaledQual(), VCFGenotypeRecord.MAX_QUAL_VALUE);
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val = g.getPhredScaledQual();
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}
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} else if ( key.equals(VCFGenotypeRecord.DEPTH_KEY) && val == null ) {
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ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
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@ -385,30 +363,34 @@ public class VCFWriter {
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} else if ( key.equals(VCFGenotypeRecord.GENOTYPE_FILTER_KEY) ) {
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val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : PASSES_FILTERS;
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}
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// TODO - do I need this?
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/*else if (val == null) {
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// generic case when there's no value associated with entry:
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val = MISSING_GENOTYPE_FIELD;
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} */
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String outputValue;
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if (writingVCF40Format) {
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VCFFormatHeaderLine.FORMAT_TYPE formatType = typeUsedForFormatString.get(key);
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Object newVal;
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if (!val.getClass().equals(String.class))
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newVal = formatType.convert(String.valueOf(val));
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else
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newVal = val;
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if (numberUsedForFormatFields.get(key)>1 && val.equals(MISSING_GENOTYPE_FIELD)) {
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// If we have a missing field but multiple values are expected, we need to construct new string with all fields.
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// for example for Number =2, string has to be ".,."
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StringBuilder v = new StringBuilder(MISSING_GENOTYPE_FIELD);
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for ( int i = 1; i < numberUsedForFormatFields.get(key); i++ ) {
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v.append(",");
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v.append(MISSING_GENOTYPE_FIELD);
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}
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newVal = v.toString();
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VCFFormatHeaderLine.FORMAT_TYPE formatType = typeUsedForFormatString.get(key);
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Object newVal;
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if (!val.getClass().equals(String.class))
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newVal = formatType.convert(String.valueOf(val));
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else
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newVal = val;
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if (numberUsedForFormatFields.get(key)>1 && val.equals(MISSING_GENOTYPE_FIELD)) {
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// If we have a missing field but multiple values are expected, we need to construct new string with all fields.
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// for example for Number =2, string has to be ".,."
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StringBuilder v = new StringBuilder(MISSING_GENOTYPE_FIELD);
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for ( int i = 1; i < numberUsedForFormatFields.get(key); i++ ) {
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v.append(",");
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v.append(MISSING_GENOTYPE_FIELD);
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}
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outputValue = formatVCFField(key, newVal);
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} else {
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outputValue = formatVCFField(key, val);
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newVal = v.toString();
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}
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String outputValue = formatVCFField(key, newVal);
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if ( outputValue != null )
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vcfG.setField(key, outputValue);
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}
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@ -428,7 +410,7 @@ public class VCFWriter {
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// Original alleles are not for reporting but only for internal bookkeeping
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if (key.equals("ORIGINAL_ALLELE_LIST"))
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continue;
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String outputValue = formatVCFField(key, elt.getValue());
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if ( outputValue != null )
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infoFields.put(key, outputValue);
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@ -436,7 +418,13 @@ public class VCFWriter {
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builder.append(referenceString);
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builder.append(contig);
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builder.append(FIELD_SEPARATOR);
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builder.append(position);
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builder.append(FIELD_SEPARATOR);
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builder.append(ID);
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builder.append(FIELD_SEPARATOR);
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builder.append(referenceFromVC);
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builder.append(FIELD_SEPARATOR);
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if ( vcfAltAlleles.size() > 0 ) {
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@ -478,7 +466,7 @@ public class VCFWriter {
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* @param builder the string builder
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* @param header the header object
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*/
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private static void addGenotypeData(StringBuilder builder, VCFHeader header,
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private void addGenotypeData(StringBuilder builder, VCFHeader header,
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String genotypeFormatString, List<VCFGenotypeEncoding>vcfAltAlleles) {
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Map<String, VCFGenotypeRecord> gMap = genotypeListToMap(mGenotypeRecords);
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@ -500,10 +488,10 @@ public class VCFWriter {
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tempStr.append(FIELD_SEPARATOR);
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if ( gMap.containsKey(genotype) ) {
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VCFGenotypeRecord rec = gMap.get(genotype);
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tempStr.append(rec.toStringEncoding(vcfAltAlleles, genotypeFormatStrings));
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tempStr.append(rec.toStringEncoding(vcfAltAlleles, genotypeFormatStrings, true));
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gMap.remove(genotype);
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} else {
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tempStr.append(VCFGenotypeRecord.stringEncodingForEmptyGenotype(genotypeFormatStrings));
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tempStr.append(VCFGenotypeRecord.stringEncodingForEmptyGenotype(genotypeFormatStrings, true));
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}
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}
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if ( gMap.size() != 0 ) {
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