Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 5:d9cbf833624e draft
planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
---|---|
date | Tue, 27 Oct 2020 12:46:55 +0000 |
parents | 386438cd4c3b |
children | 11a2a34f8a2b |
comparison
equal
deleted
inserted
replaced
4:386438cd4c3b | 5:d9cbf833624e |
---|---|
157 reads_dict[chrom_stop_pos][tag], len(pileupread.alignment.query_sequence)) | 157 reads_dict[chrom_stop_pos][tag], len(pileupread.alignment.query_sequence)) |
158 if nuc == alt: | 158 if nuc == alt: |
159 count_alt += 1 | 159 count_alt += 1 |
160 if tag not in mut_read_dict: | 160 if tag not in mut_read_dict: |
161 mut_read_dict[tag] = {} | 161 mut_read_dict[tag] = {} |
162 mut_read_dict[tag][chrom_stop_pos] = alt | 162 mut_read_dict[tag][chrom_stop_pos] = (alt, ref) |
163 else: | 163 else: |
164 mut_read_dict[tag][chrom_stop_pos] = alt | 164 mut_read_dict[tag][chrom_stop_pos] = (alt, ref) |
165 elif nuc == ref: | 165 elif nuc == ref: |
166 count_ref += 1 | 166 count_ref += 1 |
167 elif nuc == "N": | 167 elif nuc == "N": |
168 count_n += 1 | 168 count_n += 1 |
169 elif nuc == "lowQ": | 169 elif nuc == "lowQ": |