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I am using a program (Bamsplit) that relies on ssw to run, and get the following SSW error:
File "[...]/bamsplit-master/bamsplit.py", line 266, in <module>
main(parsed)
File "[...]/bamsplit-master/bamsplit.py", line 235, in main
run_bamsplit(ref, bam_in, vcf, vcf.header.samples[0], bams_out, bed_out, region)
File "[...]Software/bamsplit-master/bamsplit.py", line 225, in run_bamsplit
split_contig(contig, ref, bam_in, vcf, sample, bams_out, bed_out)
File "[...]/Software/bamsplit-master/bamsplit.py", line 211, in split_contig
last_read = split(phased_sites, ref, bam_iter, sample, bams_out, bed_out, last_read)
File "[...]/Software/bamsplit-master/bamsplit.py", line 194, in split
scores = calculate_alignment_scores(read.query_sequence, genotype)
File "[...]/Software/bamsplit-master/bamsplit.py", line 159, in calculate_alignment_scores
return [calculate_alignment_score(read, haplotype) for haplotype in genotype]
File "[...]/Software/bamsplit-master/bamsplit.py", line 159, in <listcomp>
return [calculate_alignment_score(read, haplotype) for haplotype in genotype]
File "[...]/Software/bamsplit-master/bamsplit.py", line 155, in calculate_alignment_score
alignment = aligner.align(reference=haplotype, query=read)
File "[...]/.local/lib/python3.7/site-packages/ssw-0.3.1-py3.7-linux-x86_64.egg/ssw/sswobj.py", line 99, in align
res = self._align(query, reference, flags, filter_score, filter_distance, mask_length)
File "[...].local/lib/python3.7/site-packages/ssw-0.3.1-py3.7-linux-x86_64.egg/ssw/sswobj.py", line 109, in _align
_reference = self.matrix.convert_sequence_to_ints(reference)
File "[...]/.local/lib/python3.7/site-packages/ssw-0.3.1-py3.7-linux-x86_64.egg/ssw/sswobj.py", line 64, in convert_sequence_to_ints
return _seq_type(*seq_generator)
File "[...]/.local/lib/python3.7/site-packages/ssw-0.3.1-py3.7-linux-x86_64.egg/ssw/sswobj.py", line 63, in <genexpr>
seq_generator = (self.symbol_map[symbol.upper()] for symbol in seq)
KeyError: '<'
I thought it might be a problem with "<" not being able to run through "symbol.upper()", so I attempted to manually remove all ".upper()" commands, in the sswobj.py file, but that was unable to correct the problem. Any idea on what what the issue is?
The text was updated successfully, but these errors were encountered:
I am using a program (Bamsplit) that relies on ssw to run, and get the following SSW error:
I thought it might be a problem with "<" not being able to run through "symbol.upper()", so I attempted to manually remove all ".upper()" commands, in the sswobj.py file, but that was unable to correct the problem. Any idea on what what the issue is?
The text was updated successfully, but these errors were encountered: