diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 624d06a71..18646b057 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -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;