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1) Removed hard-coded strings. Please let's use the fields defined in VCFConstants. 

2) General code cleanup.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3856 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-23 01:49:47 +00:00
parent e9d243babb
commit c5325b03be
3 changed files with 56 additions and 91 deletions
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15
java/src/org/broad/tribble/vcf/VCFReaderUtils.java
View File

@ -25,9 +25,8 @@ public class VCFReaderUtils {
Set<String> auxTags = new LinkedHashSet<String>();
// iterate over all the passed in strings
for ( String str : headerStrings ) {
if ( !str.startsWith("##") ) {
String[] strings = str.substring(1).split("\\t");
// the columns should be in order according to Richard Durbin
if ( !str.startsWith(VCFHeader.METADATA_INDICATOR) ) {
String[] strings = str.substring(1).split(VCFConstants.FIELD_SEPARATOR);
int arrayIndex = 0;
for (VCFHeader.HEADER_FIELDS field : VCFHeader.HEADER_FIELDS.values()) {
try {
@ -38,11 +37,15 @@ public class VCFReaderUtils {
}
arrayIndex++;
}
while (arrayIndex < strings.length) {
if (!strings[arrayIndex].equals("FORMAT"))
auxTags.add(strings[arrayIndex]);
if ( arrayIndex < strings.length ) {
if ( !strings[arrayIndex].equals("FORMAT") )
throw new RuntimeException("VCFReaderUtils: we were expecting column name FORMAT but we saw " + strings[arrayIndex]);
arrayIndex++;
}
while (arrayIndex < strings.length)
auxTags.add(strings[arrayIndex++]);
} else {
if ( str.startsWith("##INFO=") )
metaData.add(new VCFInfoHeaderLine(str.substring(7),version));

120
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
View File

@ -70,7 +70,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
private LineTransform transformer = null;
/**
* this method is a big hack, since I haven't gotten to updating the VCF header for the 4.0 updates
* @param reader the line reader to take header lines from
* @return the number of header lines
*/
@ -78,12 +77,12 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
public Object readHeader(LineReader reader) {
List<String> headerStrings = new ArrayList<String>();
String line = "";
String line;
try {
boolean foundHeaderVersion = false;
while ((line = reader.readLine()) != null) {
lineNo++;
if (line.startsWith("##")) {
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) {
String[] lineFields = line.substring(2).split("=");
if (lineFields.length == 2 &&
VCFHeaderVersion.isVersionString(lineFields[1]) && VCFHeaderVersion.isFormatString(lineFields[0])) {
@ -92,7 +91,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
}
headerStrings.add(line);
}
else if (line.startsWith("#")) {
else if (line.startsWith(VCFHeader.HEADER_INDICATOR)) {
if (!foundHeaderVersion) {
throw new CodecLineParsingException("We never saw a header line specifying VCF version");
}
@ -120,17 +119,14 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
headerStrings.add(line);
header = VCFReaderUtils.createHeader(headerStrings, this.version);
// load the parsing fields
Set<VCFHeaderLine> headerLines = header.getMetaData();
// setup our look-up lists for validation
for (VCFHeaderLine hl : headerLines) {
if (hl.getClass() == VCFFilterHeaderLine.class)
for ( VCFHeaderLine hl : header.getMetaData() ) {
if ( hl instanceof VCFFilterHeaderLine )
this.filterFields.add(((VCFFilterHeaderLine)hl).getName());
if (hl.getClass() == VCFFormatHeaderLine.class)
this.formatFields.put(((VCFFormatHeaderLine)hl).getName(),((VCFFormatHeaderLine)hl).getType());
if (hl.getClass() == VCFInfoHeaderLine.class)
this.infoFields.put(((VCFInfoHeaderLine)hl).getName(),((VCFInfoHeaderLine)hl).getType());
if ( hl instanceof VCFFormatHeaderLine )
this.formatFields.put(((VCFFormatHeaderLine)hl).getName(), ((VCFFormatHeaderLine)hl).getType());
if ( hl instanceof VCFInfoHeaderLine )
this.infoFields.put(((VCFInfoHeaderLine)hl).getName(), ((VCFInfoHeaderLine)hl).getType());
}
// sort the lists so we can binary search them later on
Collections.sort(filterFields);
@ -158,12 +154,12 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
private Feature reallyDecode(String line, boolean parseGenotypes) {
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.startsWith("#")) return null;
if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
if (parts == null)
parts = new String[header.getColumnCount()];
int nParts = ParsingUtils.split(line, parts, '\t');
int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR.charAt(0));
// our header cannot be null, we need the genotype sample names and counts
if (header == null) throw new IllegalStateException("VCF Header cannot be null");
@ -172,7 +168,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
if (nParts != header.getColumnCount())
throw new IllegalArgumentException("we expected " + header.getColumnCount() + " columns and we got " + nParts + " for line " + line);
return parseVCFLine(parts, parseGenotypes);
}
@ -183,21 +178,19 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
* @return an Allele
*/
private static Allele oneAllele(char index, List<Allele> alleles) {
if ( index == '.' )
if ( index == VCFConstants.EMPTY_ALLELE.charAt(0) )
return Allele.NO_CALL;
else {
int i = ((byte)index) - ZERO_CHAR;
return alleles.get(i);
}
int i = ((byte)index) - ZERO_CHAR;
return alleles.get(i);
}
/**
* parse genotype alleles from the genotype string
* @param GT
* @param alleles
* @param cache
* @return
* @param GT GT string
* @param alleles list of possible alleles
* @param cache cache of alleles for GT
* @return the allele list for the GT string
*/
private List<Allele> parseGenotypeAlleles(String GT, List<Allele> alleles, Map<String, List<Allele>> cache) {
// this should cache results [since they are immutable] and return a single object for each genotype
@ -224,8 +217,8 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
private Map<String, Object> parseInfo(String infoField, String id) {
Map<String, Object> attributes = new HashMap<String, Object>();
if ( ! infoField.equals(".") ) { // empty info field
for ( String field : Utils.split(infoField, ";") ) {
if ( !infoField.equals(VCFConstants.EMPTY_INFO_FIELD) ) {
for ( String field : Utils.split(infoField, VCFConstants.INFO_FIELD_SEPARATOR) ) {
String key;
Object value;
@ -235,31 +228,20 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
String str = field.substring(eqI+1, field.length());
// lets see if the string contains a , separator
if (str.contains(",")) {
List<Object> objects = new ArrayList<Object>();
String[] split = str.split(",");
for (String substring : split) {
VCFHeaderLineType type = infoFields.get(key);
// objects.add(type != null ? type.convert(substring,VCFCompoundHeaderLine.SupportedHeaderLineType.INFO) : substring);
objects.add(substring);
}
value = objects;
} else {
VCFHeaderLineType type = infoFields.get(key);
//value = type != null ? type.convert(str,VCFCompoundHeaderLine.SupportedHeaderLineType.INFO) : str;
if ( str.contains(",") )
value = Arrays.asList(str.split(","));
else
value = str;
}
//System.out.printf("%s %s%n", key, value);
} else {
key = field;
value = 1;
value = new Boolean(true);
}
attributes.put(key, value);
}
}
// validate the fields
validateFields(attributes.keySet(),new ArrayList(infoFields.keySet()));
validateFields(attributes.keySet(), new ArrayList<String>(infoFields.keySet()));
attributes.put(VariantContext.ID_KEY, id);
return attributes;
@ -273,7 +255,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
private void validateFields(Set<String> attributes, List<String> fields) {
// validate the info fields
if (validateFromHeader) {
int count = 0;
for (String attr : attributes)
if (Collections.binarySearch(fields,attr) < 0)
throw new VCFParserException("Unable to find field describing attribute " + attr);
@ -288,7 +269,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
private Double parseQual(String qualString) {
if ( qualString.equals(VCFConstants.MISSING_VALUE_v4) || qualString.equals(VCFConstants.MISSING_QUALITY_v3) )
return VariantContext.NO_NEG_LOG_10PERROR;
return Double.valueOf(qualString) / 10;
return Double.valueOf(qualString) / 10.0;
}
/**
@ -374,10 +355,10 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
return filterHash.get(filterString);
// otherwise we have to parse and cache the value
if ( filterString.indexOf(";") == -1 )
if ( filterString.indexOf(VCFConstants.FILTER_CODE_SEPARATOR) == -1 )
fFields.add(filterString);
else
fFields.addAll(Utils.split(filterString, ";"));
fFields.addAll(Utils.split(filterString, VCFConstants.FILTER_CODE_SEPARATOR));
filterHash.put(filterString, fFields);
@ -465,7 +446,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
Map<String, Genotype> genotypes = new LinkedHashMap<String, Genotype>(Math.max(parts.length - formatFieldLocation, 1));
// get the format keys
int nGTKeys = ParsingUtils.split(parts[formatFieldLocation], genotypeKeyArray, ':');
int nGTKeys = ParsingUtils.split(parts[formatFieldLocation], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR.charAt(0));
// cycle through the sample names
Iterator<String> sampleNameIterator = header.getGenotypeSamples().iterator();
@ -475,7 +456,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
// cycle through the genotype strings
for (int genotypeOffset = formatFieldLocation + 1; genotypeOffset < parts.length; genotypeOffset++) {
int GTValueSplitSize = ParsingUtils.split(parts[genotypeOffset], GTValueArray, ':');
int GTValueSplitSize = ParsingUtils.split(parts[genotypeOffset], GTValueArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR.charAt(0));
double GTQual = VariantContext.NO_NEG_LOG_10PERROR;
Set<String> genotypeFilters = null;
@ -491,21 +472,21 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
gtAttributes = new HashMap<String, String>(nGTKeys - 1);
for (int i = 0; i < nGTKeys; i++) {
if (i >= GTValueSplitSize) {
if (genotypeKeyArray[i].equals("GQ"))
if (genotypeKeyArray[i].equals(VCFConstants.GENOTYPE_QUALITY_KEY))
GTQual = parseQual(VCFConstants.MISSING_VALUE_v4);
else if (genotypeKeyArray[i].equals("FT")) // deal with genotype filters here
else if (genotypeKeyArray[i].equals(VCFConstants.GENOTYPE_FILTER_KEY))
genotypeFilters = parseFilters(VCFConstants.MISSING_VALUE_v4);
else
gtAttributes.put(genotypeKeyArray[i],VCFConstants.MISSING_VALUE_v4);
}
else if (genotypeKeyArray[i].equals("GT"))
else if (genotypeKeyArray[i].equals(VCFConstants.GENOTYPE_KEY))
if (i != 0)
throw new VCFParserException("Saw GT at position " + i + ", it must be at the first position for genotypes. At location = " + locAndAlleles.first);
else
genotypeAlleleLocation = i;
else if (genotypeKeyArray[i].equals("GQ"))
else if (genotypeKeyArray[i].equals(VCFConstants.GENOTYPE_QUALITY_KEY))
GTQual = parseQual(GTValueArray[i]);
else if (genotypeKeyArray[i].equals("FT")) // deal with genotype filters here
else if (genotypeKeyArray[i].equals(VCFConstants.GENOTYPE_FILTER_KEY))
genotypeFilters = parseFilters(GTValueArray[i]);
else {
if (this.version != VCFHeaderVersion.VCF4_0 && GTValueArray[i].equals(VCFConstants.MISSING_GENOTYPE_QUALITY_v3))
@ -514,7 +495,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
}
}
// validate the format fields
validateFields(gtAttributes.keySet(), new ArrayList(formatFields.keySet()));
validateFields(gtAttributes.keySet(), new ArrayList<String>(formatFields.keySet()));
}
// check to make sure we found a gentoype field
if (genotypeAlleleLocation < 0) throw new VCFParserException("Unable to find required field GT for record " + locAndAlleles.first);
@ -546,15 +527,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
static Pair<GenomeLoc,List<Allele>> clipAlleles(String contig, long position, String ref, List<Allele> unclippedAlleles) {
List<Allele> newAlleleList = new ArrayList<Allele>();
// Forward clipping (i.e. of first reference base) is not done here, but rather once a properly formed VC is obtained first.
// System.out.format("%s:%d ",contig, position);
//for (Allele a : unclippedAlleles) {
// System.out.print(a.toString());
//}
// System.out.println();
//
//
// find the preceeding string common to all alleles and the reference
boolean clipping = true;
for (Allele a : unclippedAlleles)
@ -577,7 +549,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
for (Allele a : unclippedAlleles)
newAlleleList.add(Allele.create(Arrays.copyOfRange(a.getBases(),forwardClipping,a.getBases().length-reverseClipped),a.isReference()));
// the new reference length
int refLength = ref.length() - reverseClipped;
@ -585,7 +556,6 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
newAlleleList);
}
/**
*
* @return the type of record
@ -603,6 +573,14 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
return name;
}
/**
* set the name of this codec
* @param name new name
*/
public void setName(String name) {
this.name = name;
}
public static interface LineTransform {
public String lineTransform(String line);
}
@ -615,14 +593,4 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
this.transformer = transformer;
}
/**
* set the name of this codec
* @param name
*/
public void setName(String name) {
this.name = name;
}
}

12
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
View File

@ -162,7 +162,7 @@ public class VCFWriter {
// REF
alleleMap.put(vc.getReference(), "0");
String refString = makeAlleleString(vc.getReference());
String refString = new String(vc.getReference().getBases());
mWriter.write(refString);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
@ -170,13 +170,13 @@ public class VCFWriter {
if ( vc.isVariant() ) {
Allele altAllele = vc.getAlternateAllele(0);
alleleMap.put(altAllele, "1");
String alt = makeAlleleString(altAllele);
String alt = new String(altAllele.getBases());
mWriter.write(alt);
for (int i = 1; i < vc.getAlternateAlleles().size(); i++) {
altAllele = vc.getAlternateAllele(i);
alleleMap.put(altAllele, String.valueOf(i+1));
alt = makeAlleleString(altAllele);
alt = new String(altAllele.getBases());
mWriter.write(",");
mWriter.write(alt);
}
@ -245,12 +245,6 @@ public class VCFWriter {
return s;
}
private String makeAlleleString(Allele allele) {
String s = new String(allele.getBases());
return new String(allele.getBases());
}
/**
* create the info string; assumes that no values are null
*