convert VCF ref to uppercase when read in
@@ -258,6 +258,7 @@ def read_vcf(vcf_file, ref_file):
sequences[s] = {}
refSeq = SeqIO.read(ref_file, format='fasta')
+ refSeq = refSeq.upper() #convert to uppercase to avoid unknown chars later
refSeqStr = str(refSeq.seq)
compress_seq = {'reference':refSeqStr,
