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Don't allow whitespace in the INFO field

This commit is contained in:
Eric Banks 2011-09-21 11:14:54 -04:00
parent b36d396c16
commit 174859fc68
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -215,7 +215,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
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 != null && !header.hasGenotypingData())) && nParts != NUM_STANDARD_FIELDS) ||
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);
@ -345,6 +345,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
generateException("The VCF specification requires a valid info field");
if ( !infoField.equals(VCFConstants.EMPTY_INFO_FIELD) ) {
if ( infoField.indexOf("\t") != -1 || infoField.indexOf(" ") != -1 )
generateException("The VCF specification does not allow for whitespace in the INFO field");
int infoValueSplitSize = ParsingUtils.split(infoField, infoValueArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR);
for (int i = 0; i < infoValueSplitSize; i++) {
String key;