Permalink
Browse files

Changed the rule to split records into columns

According to the specification the columns must be tab separated. I encountered an VCF file from NCBI that has spaces in the INFO column, which caused PyVCF to fail.
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
  • Loading branch information...
1 parent e63960c commit fb835a2a3023116e8477412949eb10d7459f6a39 @marcofalcioni marcofalcioni committed with casbon Nov 14, 2012
Showing with 1 addition and 1 deletion.
  1. +1 −1 vcf/parser.py
View
@@ -437,7 +437,7 @@ def _parse_alt(self, str):
def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
- row = re.split('\t| +', line)
+ row = re.split('\t+', line)
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom

0 comments on commit fb835a2

Please sign in to comment.