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My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs.

This commit is contained in:
Eric Banks 2011-09-21 22:23:28 -04:00
parent e53cb79d42
commit 8f8b59a932
3 changed files with 32 additions and 29 deletions
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38
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -115,15 +115,21 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
}
arrayIndex++;
}
boolean sawFormatTag = false;
if ( arrayIndex < strings.length ) {
if ( !strings[arrayIndex].equals("FORMAT") )
throw new TribbleException.InvalidHeader("we were expecting column name 'FORMAT' but we saw '" + strings[arrayIndex] + "'");
sawFormatTag = true;
arrayIndex++;
}
while (arrayIndex < strings.length)
while ( arrayIndex < strings.length )
auxTags.add(strings[arrayIndex++]);
if ( sawFormatTag && auxTags.size() == 0 )
throw new UserException.MalformedVCFHeader("The FORMAT field was provided but there is no genotype/sample data");
} else {
if ( str.startsWith("##INFO=") ) {
VCFInfoHeaderLine info = new VCFInfoHeaderLine(str.substring(7),version);
@ -200,28 +206,24 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @return a VariantContext
*/
public Feature decode(String line) {
return reallyDecode(line);
}
// 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(VCFHeader.HEADER_INDICATOR)) return null;
private Feature reallyDecode(String line) {
// 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(VCFHeader.HEADER_INDICATOR)) return null;
// our header cannot be null, we need the genotype sample names and counts
if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
// our header cannot be null, we need the genotype sample names and counts
if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
if (parts == null)
parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
if (parts == null)
parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
int nParts = ParsingUtils.split(line, parts, VCFConstants.FIELD_SEPARATOR_CHAR, true);
// if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data)
if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
(header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
" tokens, and saw " + nParts + " )", lineNo);
// if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data)
if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
(header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
" tokens, and saw " + nParts + " )", lineNo);
return parseVCFLine(parts);
return parseVCFLine(parts);
}
protected void generateException(String message) {

17
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
View File

@ -35,9 +35,6 @@ public class VCFHeader {
// the header string indicator
public static final String HEADER_INDICATOR = "#";
/** do we have genotying data? */
private boolean hasGenotypingData = false;
// were the input samples sorted originally (or are we sorting them)?
private boolean samplesWereAlreadySorted = true;
@ -57,17 +54,15 @@ public class VCFHeader {
* create a VCF header, given a list of meta data and auxillary tags
*
* @param metaData the meta data associated with this header
* @param genotypeSampleNames the genotype format field, and the sample names
* @param genotypeSampleNames the sample names
*/
public VCFHeader(Set<VCFHeaderLine> metaData, Set<String> genotypeSampleNames) {
mMetaData = new TreeSet<VCFHeaderLine>();
if ( metaData != null )
mMetaData.addAll(metaData);
for (String col : genotypeSampleNames) {
if (!col.equals("FORMAT"))
mGenotypeSampleNames.add(col);
}
if (genotypeSampleNames.size() > 0) hasGenotypingData = true;
mGenotypeSampleNames.addAll(genotypeSampleNames);
loadVCFVersion();
loadMetaDataMaps();
@ -157,7 +152,7 @@ public class VCFHeader {
* @return true if we have genotyping columns, false otherwise
*/
public boolean hasGenotypingData() {
return hasGenotypingData;
return mGenotypeSampleNames.size() > 0;
}
/**
@ -171,7 +166,7 @@ public class VCFHeader {
/** @return the column count */
public int getColumnCount() {
return HEADER_FIELDS.values().length + ((hasGenotypingData) ? mGenotypeSampleNames.size() + 1 : 0);
return HEADER_FIELDS.values().length + (hasGenotypingData() ? mGenotypeSampleNames.size() + 1 : 0);
}
/**

6
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -174,6 +174,12 @@ public class UserException extends ReviewedStingException {
}
}
public static class MalformedVCFHeader extends UserException {
public MalformedVCFHeader(String message) {
super(String.format("The provided VCF file has a malformed header: %s", message));
}
}
public static class ReadMissingReadGroup extends MalformedBAM {
public ReadMissingReadGroup(SAMRecord read) {
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use http://www.broadinstitute.org/gsa/wiki/index.php/ReplaceReadGroups to fix this problem", read.getReadName()));