zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-11 07:19:16 +00:00
parent 6b960bd9c5
commit fb717fe128
28 changed files with 261 additions and 253 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

79
java/src/org/broad/tribble/vcf/VCFConstants.java 100755
View File

@ -0,0 +1,79 @@
/*
* Copyright (c) 2010.
*
* 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.broad.tribble.vcf;
public final class VCFConstants {
// standard INFO/FORMAT field keys
public static final String ANCESTRAL_ALLELE_KEY = "AA";
public static final String ALLELE_COUNT_KEY = "AC";
public static final String ALLELE_FREQUENCY_KEY = "AF";
public static final String ALLELE_NUMBER_KEY = "AN";
public static final String RMS_BASE_QUALITY_KEY = "BQ";
public static final String CIGAR_KEY = "CIGAR";
public static final String DBSNP_KEY = "DB";
public static final String DEPTH_KEY = "DP";
public static final String END_KEY = "END";
public static final String GENOTYPE_FILTER_KEY = "FT";
public static final String GENOTYPE_KEY = "GT";
public static final String GENOTYPE_LIKELIHOODS_KEY = "GL";
public static final String GENOTYPE_QUALITY_KEY = "GQ";
public static final String HAPMAP2_KEY = "H2";
public static final String HAPMAP3_KEY = "H3";
public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
public static final String MAPPING_QUALITY_ZERO_KEY = "MQ0";
public static final String SAMPLE_NUMBER_KEY = "NS";
public static final String OLD_DEPTH_KEY = "RD";
public static final String STRAND_BIAS_KEY = "SB";
public static final String SOMATIC_KEY = "SOMATIC";
public static final String VALIDATED_KEY = "VALIDATED";
// separators
public static final String FORMAT_FIELD_SEPARATOR = ":";
public static final String GENOTYPE_FIELD_SEPARATOR = ":";
public static final String FIELD_SEPARATOR = "\t";
public static final String FILTER_CODE_SEPARATOR = ";";
public static final String INFO_FIELD_SEPARATOR = ";";
// missing/default values
public static final String UNFILTERED = ".";
public static final String PASSES_FILTERS_v3 = "0";
public static final String PASSES_FILTERS_v4 = "PASS";
public static final String EMPTY_ID_FIELD = ".";
public static final String EMPTY_INFO_FIELD = ".";
public static final String EMPTY_ALTERNATE_ALLELE_FIELD = ".";
public static final String MISSING_VALUE_v4 = ".";
public static final String MISSING_QUALITY_v3 = "-1";
public static final String MISSING_GENOTYPE_QUALITY_v3 = "-1";
public static final String MISSING_HAPLOTYPE_QUALITY_v3 = "-1";
public static final String MISSING_DEPTH_v3 = "-1";
public static final String EMPTY_ALLELE = ".";
public static final String EMPTY_GENOTYPE = "./.";
public static final double MAX_GENOTYPE_QUAL = 99.0;
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
}

6
java/src/org/broad/tribble/vcf/VCFGenotypeEncoding.java
View File

@ -30,8 +30,8 @@ public class VCFGenotypeEncoding {
public VCFGenotypeEncoding(String baseString, boolean allowMultipleBaseReference) {
if ((baseString.length() == 1)) {
// are we an empty (no-call) genotype?
if (baseString.equals(VCFGenotypeRecord.EMPTY_ALLELE)) {
mBases = VCFGenotypeRecord.EMPTY_ALLELE;
if (baseString.equals(VCFConstants.EMPTY_ALLELE)) {
mBases = VCFConstants.EMPTY_ALLELE;
mLength = 0;
mType = TYPE.UNCALLED;
} else if (!validBases(baseString)) {
@ -82,7 +82,7 @@ public class VCFGenotypeEncoding {
VCFGenotypeEncoding d = (VCFGenotypeEncoding) obj;
return (mType == d.mType) && (mBases.equals(d.mBases)) && (mLength == d.mLength);
}
if ( mType == TYPE.UNCALLED && obj.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) )
if ( mType == TYPE.UNCALLED && obj.toString().equals(VCFConstants.EMPTY_ALLELE) )
return true;
return false;
}

77
java/src/org/broad/tribble/vcf/VCFGenotypeRecord.java
View File

@ -15,24 +15,6 @@ import java.util.*;
*/
public class VCFGenotypeRecord {
// key names
public static final String GENOTYPE_KEY = "GT";
public static final String GENOTYPE_QUALITY_KEY = "GQ";
public static final String DEPTH_KEY = "DP";
public static final String HAPLOTYPE_QUALITY_KEY = "HQ";
public static final String GENOTYPE_FILTER_KEY = "FT";
public static final String GENOTYPE_LIKELIHOODS_KEY = "GL";
public static final String OLD_DEPTH_KEY = "RD";
// the values for empty fields
public static final String EMPTY_GENOTYPE = "./.";
public static final String EMPTY_ALLELE = ".";
public static final int MISSING_GENOTYPE_QUALITY = -1;
public static final int MISSING_DEPTH = -1;
public static final int MISSING_HAPLOTYPE_QUALITY = -1;
public static final String PASSES_FILTERS = "0";
public static final String UNFILTERED = ".";
public static final double MAX_QUAL_VALUE = 99.0;
// what kind of phasing this genotype has
@ -89,7 +71,7 @@ public class VCFGenotypeRecord {
*/
public void setField(String key, String value) {
// make sure the GT field isn't being set
if ( key.equals(GENOTYPE_KEY) )
if ( key.equals(VCFConstants.GENOTYPE_KEY) )
throw new IllegalArgumentException("Setting the GT field is not allowed as that's done internally");
mFields.put(key, value);
}
@ -132,20 +114,19 @@ public class VCFGenotypeRecord {
* @return the phred-scaled quality score
*/
public double getQual() {
return ( mFields.containsKey(GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(GENOTYPE_QUALITY_KEY)) : MISSING_GENOTYPE_QUALITY);
return ( mFields.containsKey(VCFConstants.GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(VCFConstants.GENOTYPE_QUALITY_KEY)) : Double.valueOf(VCFConstants.MISSING_GENOTYPE_QUALITY_v3));
}
public boolean isMissingQual() {
return (int)getQual() == MISSING_GENOTYPE_QUALITY;
return VCFConstants.MISSING_GENOTYPE_QUALITY_v3.equals(String.valueOf((int)getQual()));
}
public double getNegLog10PError() {
double qual = getQual();
return (qual == MISSING_GENOTYPE_QUALITY ? MISSING_GENOTYPE_QUALITY : qual / 10.0);
return (isMissingQual() ? Double.valueOf(VCFConstants.MISSING_GENOTYPE_QUALITY_v3) : getQual() / 10.0);
}
public int getReadCount() {
return ( mFields.containsKey(DEPTH_KEY) ? Integer.valueOf(mFields.get(DEPTH_KEY)) : MISSING_DEPTH);
return ( mFields.containsKey(VCFConstants.DEPTH_KEY) ? Integer.valueOf(mFields.get(VCFConstants.DEPTH_KEY)) : Integer.valueOf(VCFConstants.MISSING_DEPTH_v3));
}
public String getLocation() {
@ -203,9 +184,9 @@ public class VCFGenotypeRecord {
}
public boolean isFiltered() {
return ( mFields.get(GENOTYPE_FILTER_KEY) != null &&
!mFields.get(GENOTYPE_FILTER_KEY).equals(UNFILTERED) &&
!mFields.get(GENOTYPE_FILTER_KEY).equals(PASSES_FILTERS));
return ( mFields.get(VCFConstants.GENOTYPE_FILTER_KEY) != null &&
!mFields.get(VCFConstants.GENOTYPE_FILTER_KEY).equals(VCFConstants.UNFILTERED) &&
!mFields.get(VCFConstants.GENOTYPE_FILTER_KEY).equals(VCFConstants.PASSES_FILTERS_v3));
}
public int getPloidy() {
@ -220,7 +201,7 @@ public class VCFGenotypeRecord {
List<String> alleleStrings = new ArrayList<String>(altAlleles.size());
for (VCFGenotypeEncoding allele : mGenotypeAlleles) {
if (allele.getType() == VCFGenotypeEncoding.TYPE.UNCALLED)
alleleStrings.add(VCFGenotypeRecord.EMPTY_ALLELE);
alleleStrings.add(VCFConstants.EMPTY_ALLELE);
else
alleleStrings.add(String.valueOf((altAlleles.contains(allele)) ? altAlleles.indexOf(allele) + 1 : 0));
}
@ -269,14 +250,14 @@ public class VCFGenotypeRecord {
builder.append(toGenotypeString(altAlleles));
for ( String field : genotypeFormatStrings ) {
if ( field.equals(GENOTYPE_KEY) )
if ( field.equals(VCFConstants.GENOTYPE_KEY) )
continue;
String value = mFields.get(field);
if ( value == null && field.equals(OLD_DEPTH_KEY) )
value = mFields.get(DEPTH_KEY);
if ( value == null && field.equals(VCFConstants.OLD_DEPTH_KEY) )
value = mFields.get(VCFConstants.DEPTH_KEY);
builder.append(VCFRecord.GENOTYPE_FIELD_SEPERATOR);
builder.append(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
if ( value == null || value.equals("") )
builder.append(getMissingFieldValue(field, doVCF40));
else
@ -299,15 +280,15 @@ public class VCFGenotypeRecord {
}
public static String stringEncodingForEmptyGenotype(String[] genotypeFormatStrings, boolean doVCF40) {
StringBuilder builder = new StringBuilder();
builder.append(EMPTY_GENOTYPE);
builder.append(VCFConstants.EMPTY_GENOTYPE);
for ( String field : genotypeFormatStrings ) {
if ( field.equals(GENOTYPE_KEY) )
if ( field.equals(VCFConstants.GENOTYPE_KEY) )
continue;
// in VCF4.0, if a genotype is empty only the ./. key can be included
if (!doVCF40) {
builder.append(VCFRecord.GENOTYPE_FIELD_SEPERATOR);
builder.append(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
builder.append(getMissingFieldValue(field));
}
}
@ -324,9 +305,9 @@ public class VCFGenotypeRecord {
if (doVCF40) {
result = "."; // default missing value
// TODO - take number of elements in field as input and output corresponding .'s
if ( field.equals(GENOTYPE_LIKELIHOODS_KEY) )
if ( field.equals(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) )
result = ".,.,.";
else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
else if ( field.equals(VCFConstants.HAPLOTYPE_QUALITY_KEY) )
result = ".,.";
}
@ -334,13 +315,13 @@ public class VCFGenotypeRecord {
result = "";
if ( field.equals(GENOTYPE_QUALITY_KEY) )
result = String.valueOf(MISSING_GENOTYPE_QUALITY);
else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) )
result = String.valueOf(MISSING_DEPTH);
else if ( field.equals(GENOTYPE_FILTER_KEY) )
result = UNFILTERED;
else if ( field.equals(GENOTYPE_LIKELIHOODS_KEY) )
if ( field.equals(VCFConstants.GENOTYPE_QUALITY_KEY) )
result = String.valueOf(VCFConstants.MISSING_GENOTYPE_QUALITY_v3);
else if ( field.equals(VCFConstants.DEPTH_KEY) || field.equals(VCFConstants.OLD_DEPTH_KEY) )
result = String.valueOf(VCFConstants.MISSING_DEPTH_v3);
else if ( field.equals(VCFConstants.GENOTYPE_FILTER_KEY) )
result = VCFConstants.UNFILTERED;
else if ( field.equals(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) )
result = "0,0,0";
// TODO -- support haplotype quality
//else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
@ -351,10 +332,10 @@ public class VCFGenotypeRecord {
public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings(VCFHeaderVersion version) {
Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
result.add(new VCFFormatHeaderLine(GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
result.add(new VCFFormatHeaderLine(GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
result.add(new VCFFormatHeaderLine(DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
result.add(new VCFFormatHeaderLine(GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
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.GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
//result.add(new VCFFormatHeaderLine(HAPLOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Haplotype Quality"));
return result;
}

8
java/src/org/broad/tribble/vcf/VCFReaderUtils.java
View File

@ -149,7 +149,7 @@ public class VCFReaderUtils {
nextDivider = (genotypeString.indexOf(":") > genotypeString.length()) ? genotypeString.length() : genotypeString.indexOf(":");
parse = genotypeString.substring(0, nextDivider);
}
if (key.equals(VCFGenotypeRecord.GENOTYPE_KEY)) {
if (key.equals(VCFConstants.GENOTYPE_KEY)) {
Matcher m = gtPattern.matcher(parse);
if (!m.matches())
throw new RuntimeException("VCFReaderUtils: Unable to match GT genotype flag to it's expected pattern, the field was: " + parse);
@ -164,7 +164,7 @@ public class VCFReaderUtils {
if (nextDivider + 1 >= genotypeString.length()) nextDivider = genotypeString.length() - 1;
genotypeString = genotypeString.substring(nextDivider + 1, genotypeString.length());
}
if ( bases.size() > 0 && bases.get(0).equals(VCFGenotypeRecord.EMPTY_ALLELE) )
if ( bases.size() > 0 && bases.get(0).equals(VCFConstants.EMPTY_ALLELE) )
tagToValue.clear();
// catch some common errors, either there are too many field keys or there are two many field values
else if ( keyStrings.length != tagToValue.size() + ((bases.size() > 0) ? 1 : 0))
@ -190,8 +190,8 @@ public class VCFReaderUtils {
* @param bases the list of bases for this genotype call
*/
private static void addAllele(String alleleNumber, String[] altAlleles, char referenceBase, List<VCFGenotypeEncoding> bases) {
if (alleleNumber.equals(VCFGenotypeRecord.EMPTY_ALLELE)) {
bases.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
if (alleleNumber.equals(VCFConstants.EMPTY_ALLELE)) {
bases.add(new VCFGenotypeEncoding(VCFConstants.EMPTY_ALLELE));
} else {
int alleleValue = Integer.valueOf(alleleNumber);
// check to make sure the allele value is within bounds

94
java/src/org/broad/tribble/vcf/VCFRecord.java
View File

@ -9,36 +9,6 @@ import java.util.*;
/** the basic VCF record type */
public class VCFRecord implements Feature {
// standard info field keys
public static final String ANCESTRAL_ALLELE_KEY = "AA";
public static final String ALLELE_COUNT_KEY = "AC";
public static final String ALLELE_FREQUENCY_KEY = "AF";
public static final String ALLELE_NUMBER_KEY = "AN";
public static final String RMS_BASE_QUALITY_KEY = "BQ";
public static final String DBSNP_KEY = "DB";
public static final String DEPTH_KEY = "DP";
public static final String HAPMAP2_KEY = "H2";
public static final String HAPMAP3_KEY = "H3";
public static final String RMS_MAPPING_QUALITY_KEY = "MQ";
public static final String SAMPLE_NUMBER_KEY = "NS";
public static final String STRAND_BIAS_KEY = "SB";
// commonly used strings that are in the standard
public static final String FORMAT_FIELD_SEPERATOR = ":";
public static final String GENOTYPE_FIELD_SEPERATOR = ":";
public static final String FIELD_SEPERATOR = "\t";
public static final String FILTER_CODE_SEPERATOR = ";";
public static final String INFO_FIELD_SEPERATOR = ";";
// default values
public static final String UNFILTERED = ".";
public static final String PASSES_FILTERS = "0";
public static final String EMPTY_INFO_FIELD = ".";
public static final String EMPTY_ID_FIELD = ".";
public static final String EMPTY_ALLELE_FIELD = ".";
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
public static final int MISSING_GENOTYPE_QUALITY = -1;
// the reference base
private String mReferenceBases;
// our location
@ -176,7 +146,7 @@ public class VCFRecord implements Feature {
case INFO:
String vals[] = columnValues.get(val).split(";");
for (String alt : vals) {
if ( alt.equals(EMPTY_INFO_FIELD) )
if ( alt.equals(VCFConstants.EMPTY_INFO_FIELD) )
continue;
String keyVal[] = alt.split("=");
if ( keyVal.length == 1 )
@ -206,7 +176,7 @@ public class VCFRecord implements Feature {
* @return the ID value for this record
*/
public String getID() {
return mID == null ? EMPTY_ID_FIELD : mID;
return mID == null ? VCFConstants.EMPTY_ID_FIELD : mID;
}
/**
@ -259,14 +229,14 @@ public class VCFRecord implements Feature {
}
public double getNonRefAlleleFrequency() {
if ( mInfoFields.containsKey(ALLELE_FREQUENCY_KEY) ) {
return Double.valueOf(mInfoFields.get(ALLELE_FREQUENCY_KEY));
if ( mInfoFields.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
return Double.valueOf(mInfoFields.get(VCFConstants.ALLELE_FREQUENCY_KEY));
} else {
// this is the poor man's AF
if ( mInfoFields.containsKey(ALLELE_COUNT_KEY) && mInfoFields.containsKey(ALLELE_NUMBER_KEY)) {
String splt[] = mInfoFields.get(ALLELE_COUNT_KEY).split(",");
if ( mInfoFields.containsKey(VCFConstants.ALLELE_COUNT_KEY) && mInfoFields.containsKey(VCFConstants.ALLELE_NUMBER_KEY)) {
String splt[] = mInfoFields.get(VCFConstants.ALLELE_COUNT_KEY).split(",");
if ( splt.length > 0 ) {
return (Double.valueOf(splt[0]) / Double.valueOf(mInfoFields.get(ALLELE_NUMBER_KEY)));
return (Double.valueOf(splt[0]) / Double.valueOf(mInfoFields.get(VCFConstants.ALLELE_NUMBER_KEY)));
}
}
}
@ -304,14 +274,14 @@ public class VCFRecord implements Feature {
}
public boolean isInDBSNP() {
return ( ( mID != null && ! mID.equals(".") ) || ( mInfoFields.get(DBSNP_KEY) != null && mInfoFields.get(DBSNP_KEY).equals("1") ) );
return ( ( mID != null && ! mID.equals(".") ) || ( mInfoFields.get(VCFConstants.DBSNP_KEY) != null && mInfoFields.get(VCFConstants.DBSNP_KEY).equals("1") ) );
}
public boolean isInHapmap() {
if ( mInfoFields.get(HAPMAP2_KEY) != null && mInfoFields.get(HAPMAP2_KEY).equals("1") ) {
if ( mInfoFields.get(VCFConstants.HAPMAP2_KEY) != null && mInfoFields.get(VCFConstants.HAPMAP2_KEY).equals("1") ) {
return true;
} else {
return ( mInfoFields.get(HAPMAP3_KEY) != null && mInfoFields.get(HAPMAP3_KEY).equals("1") );
return ( mInfoFields.get(VCFConstants.HAPMAP3_KEY) != null && mInfoFields.get(VCFConstants.HAPMAP3_KEY).equals("1") );
}
}
@ -339,7 +309,7 @@ public class VCFRecord implements Feature {
}
public boolean isMissingQual() {
return (int)mQual == MISSING_GENOTYPE_QUALITY;
return VCFConstants.MISSING_GENOTYPE_QUALITY_v3.equals(String.valueOf((int)mQual));
}
/**
@ -355,13 +325,13 @@ public class VCFRecord implements Feature {
* @return an array of strings representing the filtering criteria, or UNFILTERED if none are applied
*/
public String[] getFilteringCodes() {
if (mFilterString == null) return new String[]{UNFILTERED};
return mFilterString.split(FILTER_CODE_SEPERATOR);
if (mFilterString == null) return new String[]{VCFConstants.UNFILTERED};
return mFilterString.split(VCFConstants.FILTER_CODE_SEPARATOR);
}
public boolean isFiltered() {
String[] codes = getFilteringCodes();
return !codes[0].equals(UNFILTERED) && !codes[0].equals(PASSES_FILTERS);
return !codes[0].equals(VCFConstants.UNFILTERED) && !codes[0].equals(VCFConstants.PASSES_FILTERS_v3);
}
// public boolean hasFilteringCodes() {
@ -432,8 +402,8 @@ public class VCFRecord implements Feature {
}
public void setQual(double qual) {
if ( qual < 0 && (int)qual != MISSING_GENOTYPE_QUALITY )
throw new IllegalArgumentException("Qual values cannot be negative unless they are " + MISSING_GENOTYPE_QUALITY + " ('unknown')");
if ( qual < 0 && !VCFConstants.MISSING_GENOTYPE_QUALITY_v3.equals(String.valueOf((int)qual)) )
throw new IllegalArgumentException("Qual values cannot be negative unless they are " + VCFConstants.MISSING_GENOTYPE_QUALITY_v3 + " ('unknown')");
mQual = qual;
}
@ -507,13 +477,13 @@ public class VCFRecord implements Feature {
// CHROM \t POS \t ID \t REF \t ALT \t QUAL \t FILTER \t INFO
builder.append(mContig);
builder.append(FIELD_SEPERATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(mPosition);
builder.append(FIELD_SEPERATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(getID());
builder.append(FIELD_SEPERATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(getReference());
builder.append(FIELD_SEPERATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
List<VCFGenotypeEncoding> alts = getAlternateAlleles();
if ( alts.size() > 0 ) {
builder.append(alts.get(0));
@ -522,16 +492,16 @@ public class VCFRecord implements Feature {
builder.append(alts.get(i));
}
} else {
builder.append(EMPTY_ALLELE_FIELD);
builder.append(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
}
builder.append(FIELD_SEPERATOR);
if ( (int)mQual == MISSING_GENOTYPE_QUALITY )
builder.append(MISSING_GENOTYPE_QUALITY);
builder.append(VCFConstants.FIELD_SEPARATOR);
if ( isMissingQual() )
builder.append(VCFConstants.MISSING_GENOTYPE_QUALITY_v3);
else
builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, mQual));
builder.append(FIELD_SEPERATOR);
builder.append(ParsingUtils.join(FILTER_CODE_SEPERATOR, getFilteringCodes()));
builder.append(FIELD_SEPERATOR);
builder.append(String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, mQual));
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(ParsingUtils.join(VCFConstants.FILTER_CODE_SEPARATOR, getFilteringCodes()));
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(createInfoString());
if ( mGenotypeFormatString != null && mGenotypeFormatString.length() > 0 ) {
@ -558,14 +528,14 @@ public class VCFRecord implements Feature {
if ( isFirst )
isFirst = false;
else
info.append(INFO_FIELD_SEPERATOR);
info.append(VCFConstants.INFO_FIELD_SEPARATOR);
info.append(entry.getKey());
if ( entry.getValue() != null && !entry.getValue().equals("") ) {
info.append("=");
info.append(entry.getValue());
}
}
return info.length() == 0 ? EMPTY_INFO_FIELD : info.toString();
return info.length() == 0 ? VCFConstants.EMPTY_INFO_FIELD : info.toString();
}
/**
@ -587,12 +557,12 @@ public class VCFRecord implements Feature {
}
throw new IllegalStateException("We have more genotype samples than the header specified; please check that samples aren't duplicated");
}
tempStr.append(FIELD_SEPERATOR + mGenotypeFormatString);
tempStr.append(VCFConstants.FIELD_SEPARATOR + mGenotypeFormatString);
String[] genotypeFormatStrings = mGenotypeFormatString.split(":");
for ( String genotype : header.getGenotypeSamples() ) {
tempStr.append(FIELD_SEPERATOR);
tempStr.append(VCFConstants.FIELD_SEPARATOR);
if ( gMap.containsKey(genotype) ) {
VCFGenotypeRecord rec = gMap.get(genotype);
tempStr.append(rec.toStringEncoding(mAlts, genotypeFormatStrings));

11
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -28,9 +28,8 @@ import org.apache.commons.jexl2.*;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.genotype.HardyWeinbergCalculation;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
public class VariantContextUtils {
public static JexlEngine engine = new JexlEngine();
@ -240,8 +239,8 @@ public class VariantContextUtils {
negLog10PError = Math.max(negLog10PError, vc.isVariant() ? vc.getNegLog10PError() : -1);
filters.addAll(vc.getFilters());
if ( vc.hasAttribute(VCFRecord.DEPTH_KEY) )
depth += Integer.valueOf(vc.getAttributeAsString(VCFRecord.DEPTH_KEY));
if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) )
depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY));
if ( rsID == null && vc.hasAttribute("ID") )
rsID = vc.getAttributeAsString("ID");
@ -259,7 +258,7 @@ public class VariantContextUtils {
// we care about where the call came from
if ( annotateOrigin ) {
String setValue = "";
String setValue;
if ( nFiltered == 0 && VCs.size() == priorityListOfVCs.size() ) // nothing was unfiltered
setValue = "Intersection";
else if ( nFiltered == VCs.size() ) // everything was filtered out
@ -275,7 +274,7 @@ public class VariantContextUtils {
}
if ( depth > 0 )
attributes.put(VCFRecord.DEPTH_KEY, String.valueOf(depth));
attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
if ( rsID != null )
attributes.put("ID", rsID);

30
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -178,13 +178,13 @@ public class VariantContextAdaptors {
Map<String, String> fields = new HashMap<String, String>();
for ( Map.Entry<String, String> e : vcfG.getFields().entrySet() ) {
// todo -- fixme if we put GQ and GF into key itself
if ( ! e.getKey().equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) && ! e.getKey().equals(VCFGenotypeRecord.GENOTYPE_FILTER_KEY) )
if ( ! e.getKey().equals(VCFConstants.GENOTYPE_QUALITY_KEY) && ! e.getKey().equals(VCFConstants.GENOTYPE_FILTER_KEY) )
fields.put(e.getKey(), e.getValue());
}
Set<String> genotypeFilters = new HashSet<String>();
if ( vcfG.isFiltered() ) // setup the FL genotype filter fields
genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFGenotypeRecord.GENOTYPE_FILTER_KEY).split(";")));
genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFConstants.GENOTYPE_FILTER_KEY).split(";")));
double qual = vcfG.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, qual, genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED);
@ -260,13 +260,13 @@ public class VariantContextAdaptors {
String contig = vc.getLocation().getContig();
long position = vc.getLocation().getStart();
String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : VCFRecord.EMPTY_ID_FIELD;
String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : VCFConstants.EMPTY_ID_FIELD;
double qual = vc.hasNegLog10PError() ? vc.getPhredScaledQual() : -1;
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? VCFRecord.PASSES_FILTERS : VCFRecord.UNFILTERED);
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? VCFConstants.PASSES_FILTERS_v3 : VCFConstants.UNFILTERED);
Map<Allele, VCFGenotypeEncoding> alleleMap = new HashMap<Allele, VCFGenotypeEncoding>();
alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFConstants.EMPTY_ALLELE)); // convenience for lookup
List<VCFGenotypeEncoding> vcfAltAlleles = new ArrayList<VCFGenotypeEncoding>();
for ( Allele a : vc.getAlleles() ) {
@ -313,15 +313,15 @@ public class VariantContextAdaptors {
List<String> vcfGenotypeAttributeKeys = new ArrayList<String>();
if ( vc.hasGenotypes() ) {
vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_KEY);
vcfGenotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
for ( String key : calcVCFGenotypeKeys(vc) ) {
if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) )
vcfGenotypeAttributeKeys.add(key);
}
if ( filtersWereAppliedToGenotypes )
vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_FILTER_KEY);
vcfGenotypeAttributeKeys.add(VCFConstants.GENOTYPE_FILTER_KEY);
}
String genotypeFormatString = Utils.join(VCFRecord.GENOTYPE_FIELD_SEPERATOR, vcfGenotypeAttributeKeys);
String genotypeFormatString = Utils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys);
List<VCFGenotypeRecord> genotypeObjects = new ArrayList<VCFGenotypeRecord>(vc.getGenotypes().size());
for ( Genotype g : vc.getGenotypesSortedByName() ) {
@ -335,22 +335,22 @@ public class VariantContextAdaptors {
VCFGenotypeRecord vcfG = new VCFGenotypeRecord(g.getSampleName(), encodings, phasing);
for ( String key : vcfGenotypeAttributeKeys ) {
if ( key.equals(VCFGenotypeRecord.GENOTYPE_KEY) )
if ( key.equals(VCFConstants.GENOTYPE_KEY) )
continue;
Object val = g.getAttribute(key);
// some exceptions
if ( key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ) {
if ( key.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 )
val = VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY;
val = VCFConstants.MISSING_GENOTYPE_QUALITY_v3;
else
val = Math.min(g.getPhredScaledQual(), VCFGenotypeRecord.MAX_QUAL_VALUE);
} else if ( key.equals(VCFGenotypeRecord.DEPTH_KEY) && val == null ) {
} else if ( key.equals(VCFConstants.DEPTH_KEY) && val == null ) {
ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
if ( pileup != null )
val = pileup.size();
} else if ( key.equals(VCFGenotypeRecord.GENOTYPE_FILTER_KEY) ) {
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : VCFRecord.PASSES_FILTERS;
} else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : VCFConstants.PASSES_FILTERS_v3;
}
String outputValue = formatVCFField(key, val);
@ -410,7 +410,7 @@ public class VariantContextAdaptors {
}
if ( sawGoodQual )
keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
return Utils.sorted(new ArrayList<String>(keys));
}

7
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
View File

@ -26,10 +26,7 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@ -58,7 +55,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
// Don't allow mixed types for now
private EnumSet<VariantContext.Type> ALLOWED_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION, VariantContext.Type.INDEL);
private String[] ALLOWED_FORMAT_FIELDS = {VCFGenotypeRecord.GENOTYPE_KEY, VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, VCFGenotypeRecord.DEPTH_KEY, VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY };
private String[] ALLOWED_FORMAT_FIELDS = {VCFConstants.GENOTYPE_KEY, VCFConstants.GENOTYPE_QUALITY_KEY, VCFConstants.DEPTH_KEY, VCFConstants.GENOTYPE_LIKELIHOODS_KEY };
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )

16
java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;
@ -39,10 +39,10 @@ import java.util.*;
public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
private String[] keyNames = { VCFRecord.ALLELE_NUMBER_KEY, VCFRecord.ALLELE_COUNT_KEY, VCFRecord.ALLELE_FREQUENCY_KEY };
private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFRecord.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency"),
new VCFInfoHeaderLine(VCFRecord.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
new VCFInfoHeaderLine(VCFRecord.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
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"),
new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, 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, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
@ -50,7 +50,7 @@ public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation
return null;
Map<String, Object> map = new HashMap<String, Object>();
map.put(VCFRecord.ALLELE_NUMBER_KEY, vc.getChromosomeCount());
map.put(VCFConstants.ALLELE_NUMBER_KEY, vc.getChromosomeCount());
if ( vc.getAlternateAlleles().size() > 0 ) {
ArrayList<Double> alleleFreqs = new ArrayList<Double>();
@ -60,8 +60,8 @@ public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation
alleleFreqs.add((double)vc.getChromosomeCount(allele) / (double)vc.getChromosomeCount());
}
map.put(VCFRecord.ALLELE_COUNT_KEY, alleleCounts);
map.put(VCFRecord.ALLELE_FREQUENCY_KEY, alleleFreqs);
map.put(VCFConstants.ALLELE_COUNT_KEY, alleleCounts);
map.put(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs);
}
return map;

4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@ -29,7 +29,7 @@ public class DepthOfCoverage implements InfoFieldAnnotation, StandardAnnotation
return map;
}
public List<String> getKeyNames() { return Arrays.asList(VCFRecord.DEPTH_KEY); }
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.DEPTH_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Total Depth")); }
}

3
java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
View File

@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@ -36,7 +37,7 @@ public class MappingQualityZero implements InfoFieldAnnotation, StandardAnnotati
return map;
}
public List<String> getKeyNames() { return Arrays.asList("MQ0"); }
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Total Mapping Quality Zero Reads")); }
}

4
java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@ -38,7 +38,7 @@ public class RMSMappingQuality implements InfoFieldAnnotation, StandardAnnotatio
return map;
}
public List<String> getKeyNames() { return Arrays.asList(VCFRecord.RMS_MAPPING_QUALITY_KEY); }
public List<String> getKeyNames() { return Arrays.asList(VCFConstants.RMS_MAPPING_QUALITY_KEY); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "RMS Mapping Quality")); }
}

6
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -159,7 +159,7 @@ public class VariantAnnotatorEngine {
List<ReferenceOrderedDataSource> dataSources = engine.getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) {
if ( source.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
dbAnnotations.put(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, VCFRecord.DBSNP_KEY);
dbAnnotations.put(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, VCFConstants.DBSNP_KEY);
}
else if ( source.getName().startsWith(dbPrefix) ) {
dbAnnotations.put(source.getName(), source.getName().substring(dbPrefix.length()));
@ -189,9 +189,9 @@ public class VariantAnnotatorEngine {
for ( Map.Entry<String, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getKey().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFRecord.DBSNP_KEY, dbsnp == null ? false : true);
infoAnnotations.put(VCFConstants.DBSNP_KEY, dbsnp == null ? false : true);
// annotate dbsnp id if available and not already there
if ( dbsnp != null && (!vc.hasAttribute("ID") || vc.getAttribute("ID").equals(VCFRecord.EMPTY_ID_FIELD)) )
if ( dbsnp != null && (!vc.hasAttribute("ID") || vc.getAttribute("ID").equals(VCFConstants.EMPTY_ID_FIELD)) )
infoAnnotations.put("ID", dbsnp.getRsID());
} else {
List<Object> dbRod = tracker.getReferenceMetaData(dbSet.getKey());

2
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -100,7 +100,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( genotypeFilterExps.size() > 0 )
hInfo.add(new VCFFormatHeaderLine(VCFGenotypeRecord.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
hInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, 1, VCFHeaderLineType.String, "Genotype-level filter"));
List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) {

6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
@ -153,7 +153,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
CalledGenotype cg = new CalledGenotype(sample, myAlleles, AFbasedGenotype.second);
cg.setLikelihoods(GLs.get(sample).getLikelihoods());
cg.setReadBackedPileup(contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup());
cg.putAttribute(VCFGenotypeRecord.DEPTH_KEY, contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size());
cg.putAttribute(VCFConstants.DEPTH_KEY, contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size());
cg.setPosteriors(GLs.get(sample).getPosteriors());
double[] likelihoods = GLs.get(sample).getLikelihoods();
@ -161,7 +161,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
likelihoods[refGenotype.ordinal()],
likelihoods[hetGenotype.ordinal()],
likelihoods[homGenotype.ordinal()]);
cg.putAttribute(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY, GL);
cg.putAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY, GL);
calls.put(sample, cg);
}

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -144,7 +144,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
for ( Map.Entry<String, String> dbSet : UG_engine.dbAnnotations.entrySet() )
headerInfo.add(new VCFInfoHeaderLine(dbSet.getValue(), 0, VCFHeaderLineType.Flag, (dbSet.getKey().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ? "dbSNP" : dbSet.getValue()) + " Membership"));
if ( !UAC.NO_SLOD )
headerInfo.add(new VCFInfoHeaderLine(VCFRecord.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.STRAND_BIAS_KEY, 1, VCFHeaderLineType.Float, "Strand Bias"));
// FORMAT and INFO fields
headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings(VCFHeaderVersion.VCF3_3));

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -46,7 +46,7 @@ import org.broadinstitute.sting.utils.genotype.geli.GeliGenotypeWriter;
import org.broadinstitute.sting.utils.genotype.glf.GLFGenotypeWriter;
import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeWriter;
import org.broadinstitute.sting.utils.pileup.*;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import java.io.PrintStream;
import java.util.*;
@ -113,7 +113,7 @@ public class UnifiedGenotyperEngine {
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) {
if ( source.getName().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
dbAnnotations.put(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, VCFRecord.DBSNP_KEY);
dbAnnotations.put(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, VCFConstants.DBSNP_KEY);
}
else if ( source.getName().startsWith(VariantAnnotatorEngine.dbPrefix) ) {
dbAnnotations.put(source.getName(), source.getName().substring(VariantAnnotatorEngine.dbPrefix.length()));

8
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -128,8 +128,8 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
hInfo.add(new VCFInfoHeaderLine("HetPct", 1, VCFHeaderLineType.Float, "Percent of heterozygous genotypes"));
hInfo.add(new VCFInfoHeaderLine("HomVarPct", 1, VCFHeaderLineType.Float, "Percent homozygous variant genotypes"));
hInfo.add(new VCFInfoHeaderLine("HW", 1, VCFHeaderLineType.Float, "Phred-scaled Hardy-Weinberg violation p-value"));
hInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
hInfo.add(new VCFInfoHeaderLine(VCFRecord.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
hInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, 1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
hInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
hInfo.add(new VCFFilterHeaderLine("HardyWeinbergViolation", "The validation is in Hardy-Weinberg violation"));
hInfo.add(new VCFFilterHeaderLine("HighNoCallRate", "The validation no-call rate is too high"));
hInfo.add(new VCFFilterHeaderLine("TooManyHomVars", "The validation homozygous variant rate is too high"));
@ -202,8 +202,8 @@ public class SequenomValidationConverter extends RodWalker<VCFRecord,Integer> {
int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getChromosomeCount(altAlleles.iterator().next());
if ( !isViolation && altAlleleCount > 0 )
numTrueVariants++;
infoMap.put(VCFRecord.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
infoMap.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount()));
infoMap.put(VCFConstants.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
infoMap.put(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount()));
record.addInfoFields(infoMap);
// set the id if it's a plink rod

10
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
View File

@ -101,10 +101,10 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
throw new StingException("Can not find input file: " + TRANCHE_FILENAME);
}
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_KEY); // copied from VariantsToVCF
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.DEPTH_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_KEY); // copied from VariantsToVCF
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_QUALITY_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.DEPTH_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@ -154,7 +154,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
for( int tranche = qCuts.size() - 1; tranche >= 0; tranche-- ) {
if( qual >= qCuts.get(tranche) ) {
if(tranche == qCuts.size() - 1) {
vcf.setFilterString(VCFRecord.PASSES_FILTERS);
vcf.setFilterString(VCFConstants.PASSES_FILTERS_v3);
setFilter = true;
} else {
vcf.setFilterString(filterName.get(tranche));

10
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -123,10 +123,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
}
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_KEY); // copied from VariantsToVCF
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.DEPTH_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_KEY); // copied from VariantsToVCF
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_QUALITY_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.DEPTH_KEY);
ALLOWED_FORMAT_FIELDS.add(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
// setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
@ -198,7 +198,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
vcf.addInfoField("OQ", String.format("%.2f", ((Double)vc.getPhredScaledQual())));
vcf.setQual( variantDatum.qual );
vcf.setFilterString(VCFRecord.PASSES_FILTERS);
vcf.setFilterString(VCFConstants.PASSES_FILTERS_v3);
vcfWriter.addRecord( vcf );
} else { // not a SNP or is filtered so just dump it out to the VCF file

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
View File

@ -270,10 +270,10 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
VCFRecord vcf = VariantContextAdaptors.toVCF(filteredVC, ref.getBase());
if ( filteredVC.getChromosomeCount() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", filteredVC.getChromosomeCount()));
vcf.addInfoField(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", filteredVC.getChromosomeCount()));
if ( altAlleleCountString.length() > 0 ) {
vcf.addInfoField(VCFRecord.ALLELE_COUNT_KEY, altAlleleCountString.toString());
vcf.addInfoField(VCFRecord.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
vcf.addInfoField(VCFConstants.ALLELE_COUNT_KEY, altAlleleCountString.toString());
vcf.addInfoField(VCFConstants.ALLELE_FREQUENCY_KEY, String.format("%4.2f",
Double.valueOf(altAlleleCountString.toString())/(filteredVC.getChromosomeCount())));
}
}

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/ProduceBeagleInputWalker.java
View File

@ -26,7 +26,7 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -119,8 +119,8 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
for ( String sample : samples ) {
// use sample as key into genotypes structure
Genotype genotype = genotypes.get(sample);
if (genotype.isCalled() && genotype.hasAttribute(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY)) {
String[] glArray = genotype.getAttributeAsString(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY).split(",");
if (genotype.isCalled() && genotype.hasAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY)) {
String[] glArray = genotype.getAttributeAsString(VCFConstants.GENOTYPE_LIKELIHOODS_KEY).split(",");
Double maxLikelihood = -100.0;
ArrayList<Double> likeArray = new ArrayList<Double>();

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/TrioGenotyperWalker.java
View File

@ -25,7 +25,7 @@
package org.broadinstitute.sting.playground.gatk.walkers;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
@ -159,9 +159,9 @@ public class TrioGenotyperWalker extends RefWalker<VariantContext, Integer>{
* @return
*/
private double genotypeL( List<Allele> alleles, Genotype genotypeCall ) {
String postTriplet = (String)genotypeCall.getAttribute(VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY);
String postTriplet = (String)genotypeCall.getAttribute(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
if ( postTriplet == null )
throw new StingException("BUG: TrioGenotyperWalker expected genotype likelihood triplets " + VCFGenotypeRecord.GENOTYPE_LIKELIHOODS_KEY);
throw new StingException("BUG: TrioGenotyperWalker expected genotype likelihood triplets " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
// calculate the offset -- AA => 0, AB => 1, BB => 2
int i = 0;

6
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.BinaryCodec;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.gatk.contexts.variantcontext.MutableGenotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.GenomeLocParser;
@ -191,8 +191,8 @@ public class GLFWriter implements GLFGenotypeWriter {
rms = (Double)((MutableGenotype)genotype).getAttribute(RMS_MAPPING_QUAL);
// if we can't get the depth from the read pile-up (preferred), check the tags, the VC might have it
if (genotype.hasAttribute(VCFGenotypeRecord.DEPTH_KEY) && 0 == readCount)
readCount = (Integer)((MutableGenotype)genotype).getAttribute(VCFGenotypeRecord.DEPTH_KEY);
if (genotype.hasAttribute(VCFConstants.DEPTH_KEY) && 0 == readCount)
readCount = (Integer)((MutableGenotype)genotype).getAttribute(VCFConstants.DEPTH_KEY);
addCall(GenomeLocParser.getContigInfo(vc.getLocation().getContig()), (int)vc.getLocation().getStart(), (float) rms, ref, readCount, obj);
}

6
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFParameters.java
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.genotype.vcf;
import org.broad.tribble.vcf.VCFGenotypeEncoding;
import org.broad.tribble.vcf.VCFGenotypeRecord;
import org.broad.tribble.vcf.VCFRecord;
import org.broad.tribble.vcf.VCFConstants;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
@ -76,7 +76,7 @@ class VCFParameters {
public void addAlternateBase(VCFGenotypeEncoding base) {
if ( !alternateBases.contains(base) &&
!base.toString().equals(String.valueOf(getReferenceBases()).toUpperCase()) &&
!base.toString().equals(VCFGenotypeRecord.EMPTY_ALLELE) ) {
!base.toString().equals(VCFConstants.EMPTY_ALLELE) ) {
alternateBases.add(base);
alleleCounts.add(0);
}
@ -92,7 +92,7 @@ class VCFParameters {
}
public String getFormatString() {
return Utils.join(VCFRecord.FORMAT_FIELD_SEPERATOR, formatList);
return Utils.join(VCFConstants.FORMAT_FIELD_SEPARATOR, formatList);
}
public List<VCFGenotypeRecord> getGenotypeRecords() {

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
View File

@ -91,7 +91,7 @@ public class VCFUtils {
public static VCFRecord mergeRecords(Map<VCFRecord,String> rods, Map<Pair<String, String>, String> rodNamesToSampleNames) {
VCFParameters params = new VCFParameters();
params.addFormatItem(VCFGenotypeRecord.GENOTYPE_KEY);
params.addFormatItem(VCFConstants.GENOTYPE_KEY);
// keep track of the data so we can merge them intelligently
double maxConfidence = 0.0;

93
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
View File

@ -15,7 +15,7 @@ import java.io.*;
import java.util.*;
/**
* this class writers VCF files
* this class writes VCF files
*/
public class VCFWriter {
@ -38,23 +38,6 @@ public class VCFWriter {
Map<String, Integer> numberUsedForInfoFields = new HashMap<String, Integer>();
Map<String, Integer> numberUsedForFormatFields = new HashMap<String, Integer>();
// commonly used strings that are in the standard
private final String FORMAT_FIELD_SEPARATOR = ":";
private static final String GENOTYPE_FIELD_SEPARATOR = ":";
private static final String FIELD_SEPARATOR = "\t";
private static final String FILTER_CODE_SEPARATOR = ";";
private static final String INFO_FIELD_SEPARATOR = ";";
// default values
private static final String UNFILTERED = ".";
private static final String PASSES_FILTERS_VCF3 = "0";
private static final String PASSES_FILTERS_VCF4 = "PASS";
private static final String EMPTY_INFO_FIELD = ".";
private static final String EMPTY_ID_FIELD = ".";
private static final String EMPTY_ALLELE_FIELD = ".";
private static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
private static final String MISSING_GENOTYPE_FIELD = ".";
/**
* create a VCF writer, given a file to write to
*
@ -66,7 +49,7 @@ public class VCFWriter {
public VCFWriter(File location, boolean useVCF4Format) {
this.writingVCF40Format = useVCF4Format;
this.PASSES_FILTERS_STRING = useVCF4Format ? PASSES_FILTERS_VCF4 : PASSES_FILTERS_VCF3;
this.PASSES_FILTERS_STRING = useVCF4Format ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.PASSES_FILTERS_v3;
FileOutputStream output;
try {
@ -90,7 +73,7 @@ public class VCFWriter {
}
public VCFWriter(OutputStream output, boolean useVCF4Format) {
this.writingVCF40Format = useVCF4Format;
this.PASSES_FILTERS_STRING = useVCF4Format ? PASSES_FILTERS_VCF4 : PASSES_FILTERS_VCF3;
this.PASSES_FILTERS_STRING = useVCF4Format ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.PASSES_FILTERS_v3;
mWriter = new BufferedWriter(new OutputStreamWriter(output));
}
@ -148,12 +131,12 @@ public class VCFWriter {
StringBuilder b = new StringBuilder();
b.append(VCFHeader.HEADER_INDICATOR);
for (VCFHeader.HEADER_FIELDS field : header.getHeaderFields())
b.append(field + FIELD_SEPARATOR);
b.append(field + VCFConstants.FIELD_SEPARATOR);
if (header.hasGenotypingData()) {
b.append("FORMAT" + FIELD_SEPARATOR);
b.append("FORMAT" + VCFConstants.FIELD_SEPARATOR);
for (String field : header.getGenotypeSamples())
b.append(field + FIELD_SEPARATOR);
b.append(field + VCFConstants.FIELD_SEPARATOR);
}
mWriter.write(b.toString() + "\n");
mWriter.flush(); // necessary so that writing to an output stream will work
@ -232,7 +215,7 @@ public class VCFWriter {
String contig = loc.getContig();
long position = loc.getStart();
String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : EMPTY_ID_FIELD;
String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : VCFConstants.EMPTY_ID_FIELD;
// deal with the reference
@ -243,10 +226,10 @@ public class VCFWriter {
boolean filtersWereAppliedToContext = true;
List<String> allowedGenotypeAttributeKeys = null;
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? PASSES_FILTERS_STRING : UNFILTERED);
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? PASSES_FILTERS_STRING : VCFConstants.UNFILTERED);
Map<Allele, VCFGenotypeEncoding> alleleMap = new HashMap<Allele, VCFGenotypeEncoding>();
alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFConstants.EMPTY_ALLELE)); // convenience for lookup
List<VCFGenotypeEncoding> vcfAltAlleles = new ArrayList<VCFGenotypeEncoding>();
int numTrailingBases = 0, numPaddingBases = 0;
@ -339,16 +322,16 @@ public class VCFWriter {
List<String> vcfGenotypeAttributeKeys = new ArrayList<String>();
if ( vc.hasGenotypes() ) {
vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_KEY);
vcfGenotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
for ( String key : calcVCFGenotypeKeys(vc) ) {
if ( allowedGenotypeAttributeKeys == null || allowedGenotypeAttributeKeys.contains(key) )
vcfGenotypeAttributeKeys.add(key);
}
} else if ( header.hasGenotypingData() ) {
// this needs to be done in case all samples are no-calls
vcfGenotypeAttributeKeys.add(VCFGenotypeRecord.GENOTYPE_KEY);
vcfGenotypeAttributeKeys.add(VCFConstants.GENOTYPE_KEY);
}
String genotypeFormatString = Utils.join(GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys);
String genotypeFormatString = Utils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, vcfGenotypeAttributeKeys);
List<VCFGenotypeRecord> genotypeObjects = new ArrayList<VCFGenotypeRecord>(vc.getGenotypes().size());
for ( Genotype g : vc.getGenotypesSortedByName() ) {
@ -362,27 +345,25 @@ public class VCFWriter {
VCFGenotypeRecord vcfG = new VCFGenotypeRecord(g.getSampleName(), encodings, phasing);
for ( String key : vcfGenotypeAttributeKeys ) {
if ( key.equals(VCFGenotypeRecord.GENOTYPE_KEY) )
if ( key.equals(VCFConstants.GENOTYPE_KEY) )
continue;
Object val = g.hasAttribute(key) ? g.getAttribute(key) : MISSING_GENOTYPE_FIELD;
Object val = g.hasAttribute(key) ? g.getAttribute(key) : VCFConstants.MISSING_VALUE_v4;
// some exceptions
if ( key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ) {
if ( key.equals(VCFConstants.GENOTYPE_QUALITY_KEY) ) {
if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 )
val = MISSING_GENOTYPE_FIELD;
val = VCFConstants.MISSING_VALUE_v4;
else {
// TODO - check whether we need to saturate quality to 99 as in VCF3.3 coder. For now allow unbounded values
// val = Math.min(g.getPhredScaledQual(), VCFGenotypeRecord.MAX_QUAL_VALUE);
val = g.getPhredScaledQual();
val = Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL);
}
} else if ( key.equals(VCFGenotypeRecord.DEPTH_KEY) && val == null ) {
} else if ( key.equals(VCFConstants.DEPTH_KEY) && val == null ) {
ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
if ( pileup != null )
val = pileup.size();
} else if ( key.equals(VCFGenotypeRecord.GENOTYPE_FILTER_KEY) ) {
} else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
// VCF 4.0 key for no filters is "."
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : PASSES_FILTERS_STRING;
}
@ -403,13 +384,13 @@ public class VCFWriter {
if (numberUsedForFormatFields.containsKey(key)){
int numInFormatField = numberUsedForFormatFields.get(key);
if (numInFormatField>1 && val.equals(MISSING_GENOTYPE_FIELD)) {
if (numInFormatField>1 && val.equals(VCFConstants.MISSING_VALUE_v4)) {
// If we have a missing field but multiple values are expected, we need to construct new string with all fields.
// for example for Number =2, string has to be ".,."
StringBuilder v = new StringBuilder(MISSING_GENOTYPE_FIELD);
StringBuilder v = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
for ( int i = 1; i < numInFormatField; i++ ) {
v.append(",");
v.append(MISSING_GENOTYPE_FIELD);
v.append(VCFConstants.MISSING_VALUE_v4);
}
newVal = v.toString();
}
@ -446,13 +427,13 @@ public class VCFWriter {
builder.append(contig);
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(position);
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(ID);
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(referenceFromVC);
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
if ( vcfAltAlleles.size() > 0 ) {
builder.append(vcfAltAlleles.get(0));
@ -461,21 +442,21 @@ public class VCFWriter {
builder.append(vcfAltAlleles.get(i));
}
} else {
builder.append(EMPTY_ALLELE_FIELD);
builder.append(VCFConstants.EMPTY_ALLELE);
}
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
if ( qual == -1 )
builder.append(MISSING_GENOTYPE_FIELD);
builder.append(VCFConstants.MISSING_VALUE_v4);
else
builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, qual));
builder.append(String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual));
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(filters);
builder.append(FIELD_SEPARATOR);
builder.append(VCFConstants.FIELD_SEPARATOR);
builder.append(createInfoString(infoFields));
if ( genotypeFormatString != null && genotypeFormatString.length() > 0 ) {
@ -509,12 +490,12 @@ public class VCFWriter {
}
throw new IllegalStateException("We have more genotype samples than the header specified; please check that samples aren't duplicated");
}
tempStr.append(FIELD_SEPARATOR + genotypeFormatString);
tempStr.append(VCFConstants.FIELD_SEPARATOR + genotypeFormatString);
String[] genotypeFormatStrings = genotypeFormatString.split(":");
for ( String genotype : header.getGenotypeSamples() ) {
tempStr.append(FIELD_SEPARATOR);
tempStr.append(VCFConstants.FIELD_SEPARATOR);
if ( gMap.containsKey(genotype) ) {
VCFGenotypeRecord rec = gMap.get(genotype);
String genotypeString = rec.toStringEncoding(vcfAltAlleles, genotypeFormatStrings, true);
@ -588,7 +569,7 @@ public class VCFWriter {
if ( isFirst )
isFirst = false;
else
info.append(INFO_FIELD_SEPARATOR);
info.append(VCFConstants.INFO_FIELD_SEPARATOR);
info.append(entry.getKey());
@ -612,7 +593,7 @@ public class VCFWriter {
}
}
}
return info.length() == 0 ? EMPTY_INFO_FIELD : info.toString();
return info.length() == 0 ? VCFConstants.EMPTY_INFO_FIELD : info.toString();
}
private static String formatVCFField(String key, Object val) {
@ -651,7 +632,7 @@ public class VCFWriter {
}
if ( sawGoodQual )
keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
return Utils.sorted(new ArrayList<String>(keys));
}

2
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -17,7 +17,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "e2ea7507feb66651f52320c5a46433c2" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "b2191ea11f528b9605b727d8a73dd1e1");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "596a9ec9cbc1da70481e45a5a588a41d" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "507dbd3ba6f54e066d04c4d24f59c3ab" );