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Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.

This commit is contained in:
Eric Banks 2011-07-12 01:16:21 -04:00
parent 400b0d4422
commit d7d15019dd
9 changed files with 135 additions and 67 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -41,8 +42,8 @@ import java.util.*;
public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

17
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import java.util.*;
import java.io.PrintStream;
@ -158,7 +157,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
}
// FORMAT and INFO fields
headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
headerInfo.addAll(getSupportedHeaderStrings());
// FILTER fields
if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING )
@ -167,6 +166,20 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
return headerInfo;
}
/**
* return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
* @return a set of VCF format lines
*/
private static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
return result;
}
/**
* Compute at a given locus.
*

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
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@ -358,9 +358,8 @@ public class StandardVCFWriter implements VCFWriter {
mWriter.write(key);
if ( !entry.getValue().equals("") ) {
int numVals = 1;
VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
if ( metaData != null && (metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() > 0) ) {
if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
mWriter.write("=");
mWriter.write(entry.getValue());
}

28
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java 100644
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@ -0,0 +1,28 @@
package org.broadinstitute.sting.utils.codecs.vcf;
/**
* @author ebanks
* A class representing a key=value entry for ALT fields in the VCF header
*/
public class VCFAltHeaderLine extends VCFSimpleHeaderLine {
/**
* create a VCF filter header line
*
* @param name the name for this header line
* @param description the description for this header line
*/
public VCFAltHeaderLine(String name, String description) {
super(name, description, SupportedHeaderLineType.ALT);
}
/**
* create a VCF info header line
*
* @param line the header line
* @param version the vcf header version
*/
protected VCFAltHeaderLine(String line, VCFHeaderVersion version) {
super(line, version, SupportedHeaderLineType.ALT);
}
}

3
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
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@ -89,6 +89,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
* @param count the count for this header line
* @param type the type for this header line
* @param description the description for this header line
* @param lineType the header line type
*/
protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
super(lineType.toString(), "");
@ -108,6 +109,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
* @param count the count type for this header line
* @param type the type for this header line
* @param description the description for this header line
* @param lineType the header line type
*/
protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
super(lineType.toString(), "");
@ -124,6 +126,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
*
* @param line the header line
* @param version the VCF header version
* @param lineType the header line type
*
*/
protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {

48
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
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@ -1,19 +1,10 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import java.util.Arrays;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* @author ebanks
* A class representing a key=value entry for FILTER fields in the VCF header
*/
public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine {
private String name;
private String description;
public class VCFFilterHeaderLine extends VCFSimpleHeaderLine {
/**
* create a VCF filter header line
@ -22,12 +13,7 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
* @param description the description for this header line
*/
public VCFFilterHeaderLine(String name, String description) {
super("FILTER", "");
this.name = name;
this.description = description;
if ( name == null || description == null )
throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
super(name, description, SupportedHeaderLineType.FILTER);
}
/**
@ -37,34 +23,6 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
* @param version the vcf header version
*/
protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
super("FILTER", "");
Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
name = mapping.get("ID");
description = mapping.get("Description");
if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided
description = UNBOUND_DESCRIPTION;
}
protected String toStringEncoding() {
Map<String,Object> map = new LinkedHashMap<String,Object>();
map.put("ID", name);
map.put("Description", description);
return "FILTER=" + VCFHeaderLine.toStringEncoding(map);
}
public boolean equals(Object o) {
if ( !(o instanceof VCFFilterHeaderLine) )
return false;
VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
return name.equals(other.name) &&
description.equals(other.description);
}
public String getName() {
return name;
}
public String getDescription() {
return description;
super(line, version, SupportedHeaderLineType.FILTER);
}
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
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@ -17,7 +17,7 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
}
public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
super(name, count, type, description, SupportedHeaderLineType.INFO);
super(name, count, type, description, SupportedHeaderLineType.FORMAT);
}
protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {

81
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java 100644
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@ -0,0 +1,81 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import java.util.Arrays;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* @author ebanks
* A class representing a key=value entry for simple VCF header types
*/
public abstract class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine {
public enum SupportedHeaderLineType {
FILTER, ALT;
}
private String name;
private String description;
// our type of line, i.e. filter, alt, etc
private final SupportedHeaderLineType lineType;
/**
* create a VCF filter header line
*
* @param name the name for this header line
* @param description the description for this header line
* @param lineType the header line type
*/
public VCFSimpleHeaderLine(String name, String description, SupportedHeaderLineType lineType) {
super(lineType.toString(), "");
this.lineType = lineType;
this.name = name;
this.description = description;
if ( name == null || description == null )
throw new IllegalArgumentException(String.format("Invalid VCFSimpleHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
}
/**
* create a VCF info header line
*
* @param line the header line
* @param version the vcf header version
* @param lineType the header line type
*/
protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
super(lineType.toString(), "");
this.lineType = lineType;
Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
name = mapping.get("ID");
description = mapping.get("Description");
if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided
description = UNBOUND_DESCRIPTION;
}
protected String toStringEncoding() {
Map<String,Object> map = new LinkedHashMap<String,Object>();
map.put("ID", name);
map.put("Description", description);
return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
}
public boolean equals(Object o) {
if ( !(o instanceof VCFSimpleHeaderLine) )
return false;
VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
return name.equals(other.name) &&
description.equals(other.description);
}
public String getName() {
return name;
}
public String getDescription() {
return description;
}
}

15
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
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@ -180,19 +180,4 @@ public class VCFUtils {
return new HashSet<VCFHeaderLine>(map.values());
}
/**
* return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
* @return a set of VCF format lines
*/
public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, -1, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
return result;
}
}