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Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator. 

Also, moved the flag indicating VCF4.0 to the VCFWriter constructor.

 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-06-29 16:43:00 +00:00
parent 801b47c6e9
commit 3ca2b7374b
3 changed files with 89 additions and 17 deletions
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3
java/src/org/broad/tribble/vcf/VCFFormatHeaderLine.java
View File

@ -22,7 +22,8 @@ public class VCFFormatHeaderLine extends VCFHeaderLine {
public Object convert(String value) {
switch (this) {
case Integer:
return java.lang.Integer.valueOf(value); // the java.lang is needed since we use Integer as a enum name
// Take care of case when string might have say "43.0" but we request an Integer.
return Math.round(java.lang.Float.valueOf(value)); // the java.lang is needed since we use Integer as a enum name
case Float:
return java.lang.Float.valueOf(value);
case String:

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
View File

@ -85,7 +85,8 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
// Open output file specified by output VCF ROD
vcfWriter = new VCFWriter(new File(OUTPUT_FILE));
vcfWriter = new VCFWriter(new File(OUTPUT_FILE), true);
for( final ReferenceOrderedDataSource source : dataSources ) {
final RMDTrack rod = source.getReferenceOrderedData();

100
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
View File

@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.genotype.CalledGenotype;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -26,9 +27,17 @@ public class VCFWriter {
// the print stream we're writting to
BufferedWriter mWriter;
private boolean writingVCF40Format;
// our genotype sample fields
private static final List<VCFGenotypeRecord> mGenotypeRecords = new ArrayList<VCFGenotypeRecord>();
// Properties only used when using VCF4.0 encoding
Map<String, VCFFormatHeaderLine.FORMAT_TYPE> typeUsedForFormatString = new HashMap<String, VCFFormatHeaderLine.FORMAT_TYPE>();
Map<String, VCFInfoHeaderLine.INFO_TYPE> typeUsedForInfoFields = new HashMap<String, VCFInfoHeaderLine.INFO_TYPE>();
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 = ":";
@ -44,7 +53,7 @@ public class VCFWriter {
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_QUALITY = ".";
private static final String MISSING_GENOTYPE_FIELD = ".";
/**
* create a VCF writer, given a file to write to
@ -52,6 +61,11 @@ public class VCFWriter {
* @param location the file location to write to
*/
public VCFWriter(File location) {
this(location, false);
}
public VCFWriter(File location, boolean useVCF4Format) {
this.writingVCF40Format = useVCF4Format;
FileOutputStream output;
try {
output = new FileOutputStream(location);
@ -68,26 +82,47 @@ public class VCFWriter {
* @param output the file location to write to
*/
public VCFWriter(OutputStream output) {
// use VCF3.3 by default
this(output, false);
}
public VCFWriter(OutputStream output, boolean useVCF4Format) {
this.writingVCF40Format = useVCF4Format;
mWriter = new BufferedWriter(new OutputStreamWriter(output));
}
public void writeHeader(VCFHeader header) {
// use 3.3 format by default
// TODO - update to true once 4.0 is on by default
writeHeader(header, false);
}
public void writeHeader(VCFHeader header, boolean useVCF4Format) {
this.mHeader = header;
try {
// the file format field needs to be written first
TreeSet<VCFHeaderLine> nonFormatMetaData = new TreeSet<VCFHeaderLine>();
for ( VCFHeaderLine line : header.getMetaData() ) {
if (useVCF4Format) {
if (writingVCF40Format) {
if ( line.getKey().equals(VCFHeaderVersion.VCF4_0.getFormatString()) ) {
mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeaderVersion.VCF4_0.getFormatString() + "=" + VCFHeaderVersion.VCF4_0.getVersionString() + "\n");
} else {
nonFormatMetaData.add(line);
}
// Record, if line corresponds to a FORMAT field, which type will be used for writing value
if (line.getClass() == VCFFormatHeaderLine.class) {
VCFFormatHeaderLine a = (VCFFormatHeaderLine)line;
String key = a.getmName();
typeUsedForFormatString.put(key,a.getmType());
int num = a.getmCount();
numberUsedForFormatFields.put(key,num);
} else if (line.getClass() == VCFInfoHeaderLine.class) {
VCFInfoHeaderLine a = (VCFInfoHeaderLine)line;
String key = a.getmName();
typeUsedForInfoFields.put(key,a.getmType());
int num = a.getmCount();
numberUsedForInfoFields.put(key, num);
}
}
else {
if ( line.getKey().equals(VCFHeaderVersion.VCF3_3.getFormatString()) ) {
@ -184,7 +219,6 @@ public class VCFWriter {
// CHROM \t POS \t ID \t REF \t ALT \t QUAL \t FILTER \t INFO
GenomeLoc loc = vc.getLocation();
//String referenceBases = new String(vc.getReference().getBases());
String contig = loc.getContig();
long position = loc.getStart();
@ -288,6 +322,7 @@ public class VCFWriter {
if ( key.equals(VCFGenotypeRecord.GENOTYPE_KEY) )
continue;
Object val = g.getAttribute(key);
// some exceptions
if ( key.equals(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY) ) {
@ -295,6 +330,7 @@ public class VCFWriter {
val = VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY;
else
val = Math.min(g.getPhredScaledQual(), VCFGenotypeRecord.MAX_QUAL_VALUE);
} else if ( key.equals(VCFGenotypeRecord.DEPTH_KEY) && val == null ) {
ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
if ( pileup != null )
@ -303,7 +339,29 @@ public class VCFWriter {
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : PASSES_FILTERS;
}
String outputValue = formatVCFField(key, val);
String outputValue;
if (writingVCF40Format) {
VCFFormatHeaderLine.FORMAT_TYPE formatType = typeUsedForFormatString.get(key);
Object newVal;
if (!val.getClass().equals(String.class))
newVal = formatType.convert(String.valueOf(val));
else
newVal = val;
if (numberUsedForFormatFields.get(key)>1 && val.equals(MISSING_GENOTYPE_FIELD)) {
// 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);
for ( int i = 1; i < numberUsedForFormatFields.get(key); i++ ) {
v.append(",");
v.append(MISSING_GENOTYPE_FIELD);
}
newVal = v.toString();
}
outputValue = formatVCFField(key, newVal);
} else {
outputValue = formatVCFField(key, val);
}
if ( outputValue != null )
vcfG.setField(key, outputValue);
}
@ -320,6 +378,7 @@ public class VCFWriter {
if ( key.equals("ID") )
continue;
//TODO - fixme
String outputValue = formatVCFField(key, elt.getValue());
if ( outputValue != null )
infoFields.put(key, outputValue);
@ -327,7 +386,6 @@ public class VCFWriter {
builder.append(referenceString);
builder.append(FIELD_SEPARATOR);
@ -344,7 +402,7 @@ public class VCFWriter {
if ( qual == -1 )
builder.append(MISSING_GENOTYPE_QUALITY);
builder.append(MISSING_GENOTYPE_FIELD);
else
builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, qual));
@ -424,9 +482,10 @@ public class VCFWriter {
/**
* create the info string
*
* @param infoFields a map of info fields
* @return a string representing the infomation fields
*/
static protected String createInfoString(Map<String,String> infoFields) {
protected String createInfoString(Map<String,String> infoFields) {
StringBuffer info = new StringBuffer();
boolean isFirst = true;
for (Map.Entry<String, String> entry : infoFields.entrySet()) {
@ -436,8 +495,18 @@ public class VCFWriter {
info.append(INFO_FIELD_SEPARATOR);
info.append(entry.getKey());
if ( entry.getValue() != null && !entry.getValue().equals("") ) {
info.append("=");
info.append(entry.getValue());
int numVals = 1;
if (this.writingVCF40Format) {
numVals = numberUsedForInfoFields.get(entry.getKey());
// take care of unbounded encoding
if (numVals == VCFInfoHeaderLine.UNBOUNDED)
numVals = 1;
}
if (numVals > 0) {
info.append("=");
info.append(entry.getValue());
}
}
}
return info.length() == 0 ? EMPTY_INFO_FIELD : info.toString();
@ -447,8 +516,9 @@ public class VCFWriter {
String result;
if ( val == null )
result = VCFGenotypeRecord.getMissingFieldValue(key);
else if ( val instanceof Double )
else if ( val instanceof Double ) {
result = String.format("%.2f", (Double)val);
}
else if ( val instanceof Boolean )
result = (Boolean)val ? "" : null; // empty string for true, null for false
else if ( val instanceof List ) {