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Sean Davis committed de8bd79

Fixed encoding issues associated with richly-annotated vcf files (some bad bytes)

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  • Parent commits 9a46114

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Files changed (2)

File seqtools/commands/vcfCommands.py

 
 def meltVcf(opts):
     if(opts.vcf):
-        v = vcf.Reader(filename=opts.vcf)
+        f = open(opts.vcf,mode='r',errors='ignore')
+        v = vcf.Reader(f)
     else:
         v = vcf.Reader(sys.stdin)
     if(opts.outfile):
 
 def RNAcounts(opts):
     if(opts.vcf):
-        v = vcf.Reader(filename=opts.vcf)
+        f = open(opts.vcf,mode='r',errors='ignore')
+        v = vcf.Reader(f)
     else:
         v = vcf.Reader(sys.stdin)
     if(opts.outfile):
 from setuptools import setup, find_packages
 import sys, os, glob
 
-version = '0.4.2'
+version = '0.4.3'
 
 setup(name='seqtools',
       version=version,