| /dports/biology/seqtk/seqtk-1.3/ |
| H A D | seqtk.c | 117 unsigned char seq_nt16_table[256] = { variable
402 na = seq->seq.s[beg]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb]; in stk_comp()
407 na = seq->seq.s[i+1]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb]; in stk_comp()
461 c = seq_nt16_table[b]; in stk_randbase()
530 c = seq_nt16_table[c]; in stk_hety()
677 c[0] = seq_nt16_table[c[0]]; c[1] = seq_nt16_table[c[1]]; in stk_mergefa()
870 if (bitcnt_table[seq_nt16_table[b]] == 2) in stk_listhet()
887 if (seq_nt16_table[(int)ks->seq.s[k]] == 15) { in find_next_cut()
891 if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score; in find_next_cut()
897 if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score; in find_next_cut()
[all …]
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| /dports/biology/py-pysam/pysam-0.18.0/pysam/ |
| H A D | htslib_util.c | 97 return seq_nt16_table[s]; in pysam_translate_sequence()
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| /dports/biology/py-pysam/pysam-0.18.0/samtools/ |
| H A D | bam2bcf_indel.c | 270 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_call_gap_prep()
309 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_call_gap_prep()
313 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
316 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
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| H A D | bam2bcf_indel.c.pysam.c | 272 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_call_gap_prep()
311 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_call_gap_prep()
315 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
318 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
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| H A D | bam_md.c | 86 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
130 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
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| H A D | bam_md.c.pysam.c | 88 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
132 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
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| H A D | padding.c | 148 int i = seq_nt16_table[(int)base]; in load_unpadded_ref()
181 int i = seq_nt16_table[(int)base]; in get_unpadded_len()
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| H A D | padding.c.pysam.c | 150 int i = seq_nt16_table[(int)base]; in load_unpadded_ref()
183 int i = seq_nt16_table[(int)base]; in get_unpadded_len()
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| /dports/biology/samtools/samtools-1.14/ |
| H A D | bam2bcf_indel.c | 270 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_call_gap_prep()
309 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_call_gap_prep()
313 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
316 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
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| H A D | bam_md.c | 86 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
130 c2 = seq_nt16_table[(uint8_t)ref[rpos+j]]; in bam_fillmd1_core()
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| H A D | padding.c | 148 int i = seq_nt16_table[(int)base]; in load_unpadded_ref()
181 int i = seq_nt16_table[(int)base]; in get_unpadded_len()
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| /dports/biology/stacks/stacks-2.4/htslib/ |
| H A D | realn.c | 49 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(int)ref[x+j]]; in sam_cap_mapq()
153 r[i-xb] = seq_nt16_int[seq_nt16_table[(int)ref[i]]]; in sam_prob_realn()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
| H A D | realn.c | 49 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(int)ref[x+j]]; in sam_cap_mapq()
153 r[i-xb] = seq_nt16_int[seq_nt16_table[(int)ref[i]]]; in sam_prob_realn()
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 295 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_cgp_ref_sample()
414 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_cgp_l_run()
419 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
422 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | bam2bcf_indel.c | 295 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_cgp_ref_sample()
414 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_cgp_l_run()
419 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
422 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | bam2bcf_indel.c | 295 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_cgp_ref_sample()
414 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_cgp_l_run()
419 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
422 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
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| H A D | bam2bcf_indel.c.pysam.c | 297 ref0[i] = seq_nt16_table[(int)ref[i+left]]; in bcf_cgp_ref_sample()
416 int c = seq_nt16_table[(int)ref[pos + 1]]; in bcf_cgp_l_run()
421 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
424 if (seq_nt16_table[(int)ref[i]] != c) break; in bcf_cgp_l_run()
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| /dports/biology/vt/vt-0.57721/lib/htslib/ |
| H A D | realn.c | 53 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(int)ref[x+j]]; in sam_cap_mapq()
210 tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; in sam_prob_realn()
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| /dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
| H A D | realn.c | 53 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(int)ref[x+j]]; in sam_cap_mapq()
210 tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; in sam_prob_realn()
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| /dports/biology/py-pysam/pysam-0.18.0/htslib/ |
| H A D | realn.c | 55 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(unsigned char)ref[x+j]]; in sam_cap_mapq()
233 tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; in sam_prob_realn()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
| H A D | realn.c | 55 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(unsigned char)ref[x+j]]; in sam_cap_mapq()
213 tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; in sam_prob_realn()
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| /dports/biology/htslib/htslib-1.14/ |
| H A D | realn.c | 55 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(unsigned char)ref[x+j]]; in sam_cap_mapq()
233 tref[i-xb] = seq_nt16_int[seq_nt16_table[(unsigned char)ref[i]]]; in sam_prob_realn()
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | hts.h | 176 extern const unsigned char seq_nt16_table[256];
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| /dports/biology/pbbam/pbbam-0.18.0/src/ |
| H A D | BamRecordBuilder.cpp | 120 s[i >> 1] |= (seq_nt16_table[static_cast<int>(sequence_.at(i))] << ((~i & 1) << 2)); in BuildInPlace()
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| /dports/biology/kallisto/kallisto-0.46.1/ext/htslib/htslib/ |
| H A D | hts.h | 309 extern const unsigned char seq_nt16_table[256];
|