| /dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
| H A D | bam2bcf_indel.c | 193 int c = bam_nt16_table[(int)ref[pos + 1]]; in bcf_call_gap_prep()
197 if (bam_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
200 if (bam_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
257 ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; in bcf_call_gap_prep()
267 ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; in bcf_call_gap_prep()
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| H A D | bam_md.c | 28 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
66 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
128 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_cap_mapQ()
225 r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]]; in bam_prob_realn_core()
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| H A D | bam_plcmd.c | 142 g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c); in glt3_func()
191 if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.'; in pileup_seq()
264 glf1_t *g = bam_maqcns_glfgen(n, pu, bam_nt16_table[rb], d->c); in pileup_func()
277 if (!(bam_nt16_table[rb] != 15 && cns>>28 != 15 && cns>>28 != bam_nt16_table[rb])) { // not a SNP in pileup_func()
734 ref16 = bam_nt16_table[_ref0]; in mpileup()
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| H A D | bam_import.c | 24 unsigned char bam_nt16_table[256] = { variable
345 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2); in sam_read1()
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| H A D | bam.h | 266 extern unsigned char bam_nt16_table[256];
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| H A D | bam_maqcns.c | 468 ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; in bam_maqindel()
478 ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]]; in bam_maqindel()
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | bam_md.c | 38 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
74 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
152 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_cap_mapQ()
250 r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]]; in bam_prob_realn_core()
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| H A D | bam2bcf_indel.c | 211 ref0[i] = bam_nt16_table[(int)ref[i+left]]; in bcf_call_gap_prep()
250 int c = bam_nt16_table[(int)ref[pos + 1]]; in bcf_call_gap_prep()
254 if (bam_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
257 if (bam_nt16_table[(int)ref[i]] != c) break; in bcf_call_gap_prep()
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| H A D | bam_plcmd.c | 38 if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.'; in pileup_seq()
336 ref16 = bam_nt16_table[_ref0]; in mpileup()
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| H A D | bam_tview.c | 62 extern unsigned char bam_nt16_table[256]; in tv_pl_func()
79 bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr); in tv_pl_func()
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| H A D | bam_import.c | 27 unsigned char bam_nt16_table[256] = { variable
369 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2); in sam_read1()
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| H A D | bam.h | 279 extern unsigned char bam_nt16_table[256];
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| /dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
| H A D | bam_md.c | 38 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
74 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_fillmd1_core()
152 int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; in bam_cap_mapQ()
250 r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]]; in bam_prob_realn_core()
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| H A D | bam_plcmd.c | 37 if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.'; in pileup_seq()
307 ref16 = bam_nt16_table[_ref0]; in mpileup()
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| H A D | bam_tview.c | 62 extern unsigned char bam_nt16_table[256]; in tv_pl_func()
79 bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr); in tv_pl_func()
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| H A D | bam_import.c | 24 unsigned char bam_nt16_table[256] = { variable
350 p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2); in sam_read1()
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| H A D | bam.h | 279 extern unsigned char bam_nt16_table[256];
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/util_assembly_consensus/ |
| H A D | AssemblyConsensusAlgorithmSamtools.cpp | 100 bcf_call_glfgen(n, pl, bam_nt16_table[rb], bca, &bcr); in processBase()
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/ |
| H A D | SamtoolsAdapter.cpp | 86 qint8 value = bam_nt16_table[sequence[2 * i]] << 4; in sequence2samtools()
88 value |= bam_nt16_table[sequence[2 * i + 1]] & 0xf; in sequence2samtools()
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| /dports/biology/stringtie/stringtie-2.1.1/gclib/ |
| H A D | GBam.cpp | 154 p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2); in add_sequence()
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| /dports/biology/gffread/gffread-0.12.7/gclib/ |
| H A D | GBam.cpp | 157 p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2); in add_sequence()
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| /dports/biology/emboss/EMBOSS-6.6.0/ajax/core/ |
| H A D | ajassemwrite.c | 533 unsigned char bam_nt16_table[256] = in assemoutWriteBamAlignment() local
643 dpos[i/2] |= bam_nt16_table[(ajuint)s[i]] << 4*(1-i%2); in assemoutWriteBamAlignment()
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| H A D | ajseqbam.c | 89 unsigned char bam_nt16_table[256] = variable
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| H A D | ajseqwrite.c | 7139 unsigned char bam_nt16_table[256] = in seqWriteBam() local
7237 dpos[i/2] |= bam_nt16_table[(ajuint)s[i]] << 4*(1-i%2); in seqWriteBam()
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