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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/
H A Dstrsearch.hpp301 void QueueAdd(vector<int>& in_queue, int qbeg, int val);
425 void CTextFsm<MatchType>::QueueAdd(vector<int>& in_queue, int qbeg, int val) in QueueAdd() argument
429 q = in_queue [qbeg]; in QueueAdd()
431 in_queue [qbeg] = val; in QueueAdd()
443 int qbeg, r, s, state; in ComputeFail() local
446 qbeg = 0; in ComputeFail()
456 QueueAdd(state_queue, qbeg, s); in ComputeFail()
459 while (state_queue [qbeg] != 0) { in ComputeFail()
460 r = state_queue [qbeg]; in ComputeFail()
461 qbeg = r; in ComputeFail()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/
H A Dstrsearch.hpp301 void QueueAdd(vector<int>& in_queue, int qbeg, int val);
425 void CTextFsm<MatchType>::QueueAdd(vector<int>& in_queue, int qbeg, int val) in QueueAdd() argument
429 q = in_queue [qbeg]; in QueueAdd()
431 in_queue [qbeg] = val; in QueueAdd()
443 int qbeg, r, s, state; in ComputeFail() local
446 qbeg = 0; in ComputeFail()
456 QueueAdd(state_queue, qbeg, s); in ComputeFail()
459 while (state_queue [qbeg] != 0) { in ComputeFail()
460 r = state_queue [qbeg]; in ComputeFail()
461 qbeg = r; in ComputeFail()
[all …]
/dports/biology/bwa/bwa-0.7.17/
H A Dbwtsw2_chain.c10 int qbeg, qend; member
15 #define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)
28 int x = p->qbeg - q->qbeg; // always positive in KSORT_INIT()
65 q->qbeg = p->beg; q->qend = p->end; in bsw2_chain_filter()
75 int tmp = p->qbeg; in bsw2_chain_filter()
76 p->qbeg = len - p->qend; p->qend = len - tmp; in bsw2_chain_filter()
H A Dbwamem.c170 int32_t qbeg, len; member
197 …if (p->qbeg >= c->seeds[0].qbeg && p->qbeg + p->len <= qend && p->rbeg >= c->seeds[0].rbeg && p->r… in KBTREE_INIT()
200 x = p->qbeg - last->qbeg; // always non-negtive in KBTREE_INIT()
220 else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end; in mem_chain_weight()
221 end = end > s->qbeg + s->len? end : s->qbeg + s->len; in mem_chain_weight()
284 s.qbeg = p->info>>32; in mem_chain()
579 qb = s->qbeg, qe = s->qbeg + s->len; in mem_seed_sw()
646 b = t->rbeg - (t->qbeg + cal_max_gap(opt, t->qbeg)); in mem_chain2aln()
697 …if (s->qbeg <= t->qbeg && s->qbeg + s->len - t->qbeg >= s->len>>2 && t->qbeg - s->qbeg != t->rbeg … in mem_chain2aln()
698 …if (t->qbeg <= s->qbeg && t->qbeg + t->len - s->qbeg >= s->len>>2 && s->qbeg - t->qbeg != s->rbeg … in mem_chain2aln()
[all …]
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dblast2sam.pl13 my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq);
33 @cigar = (); $qbeg = 0;
39 unless ($qbeg) {
40 $qbeg = $1;
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dbam2bcf_indel.c274 int qbeg, qend, tbeg, tend, sc; in bcf_call_gap_prep() local
285 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
286 query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)]; in bcf_call_gap_prep()
290 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep()
293 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep()
294 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep()
295 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep()
296 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep()
299 (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0); in bcf_call_gap_prep()
305 (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0); in bcf_call_gap_prep()
[all …]
/dports/biology/samtools/samtools-1.14/misc/
H A Dblast2sam.pl38 my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq);
65 @cigar = (); $qbeg = 0;
71 unless ($qbeg) {
72 $qbeg = $1;
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam2bcf_indel.c327 int qbeg, qend, tbeg, tend, sc, kk; in bcf_call_gap_prep() local
344 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
345 query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)]; in bcf_call_gap_prep()
349 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep()
352 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep()
353 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep()
354 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep()
355 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep()
358 (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0); in bcf_call_gap_prep()
364 (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0); in bcf_call_gap_prep()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam2bcf_indel.c388 int qbeg, qend, sc, kk; in bcf_call_gap_prep() local
399 qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left, 0, &tbeg); in bcf_call_gap_prep()
406 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
407 query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; in bcf_call_gap_prep()
411 if (qend < qbeg) { in bcf_call_gap_prep()
415 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep()
418 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep()
419 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep()
420 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep()
421 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep()
[all …]
H A Dbam2bcf_indel.c.pysam.c390 int qbeg, qend, sc, kk; in bcf_call_gap_prep() local
401 qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left, 0, &tbeg); in bcf_call_gap_prep()
408 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
409 query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; in bcf_call_gap_prep()
413 if (qend < qbeg) { in bcf_call_gap_prep()
417 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep()
420 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep()
421 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep()
422 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep()
423 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep()
[all …]
/dports/biology/samtools/samtools-1.14/
H A Dbam2bcf_indel.c388 int qbeg, qend, sc, kk; in bcf_call_gap_prep() local
399 qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left, 0, &tbeg); in bcf_call_gap_prep()
406 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
407 query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)]; in bcf_call_gap_prep()
411 if (qend < qbeg) { in bcf_call_gap_prep()
415 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep()
418 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep()
419 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep()
420 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep()
421 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep()
[all …]
/dports/biology/bcftools/bcftools-1.14/
H A Dbam2bcf_indel.c498 int qbeg, int qend, in bcf_cgp_align_score() argument
519 if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) in bcf_cgp_align_score()
523 for (l = qbeg; l < qend; ++l) { in bcf_cgp_align_score()
529 qq[l - qbeg] = qval; in bcf_cgp_align_score()
535 query, qend - qbeg, qq, &apf, 0, 0); in bcf_cgp_align_score()
543 l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; in bcf_cgp_align_score()
847 int qbeg, qpos, qend, tbeg, tend, kk; in bcf_call_gap_prep() local
881 0, &tend) - qbeg; in bcf_call_gap_prep()
891 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
919 for (l = 0; l < qend - qbeg; ++l) in bcf_call_gap_prep()
[all …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dbam2bcf_indel.c498 int qbeg, int qend, in bcf_cgp_align_score() argument
519 if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) in bcf_cgp_align_score()
523 for (l = qbeg; l < qend; ++l) { in bcf_cgp_align_score()
529 qq[l - qbeg] = qval; in bcf_cgp_align_score()
535 query, qend - qbeg, qq, &apf, 0, 0); in bcf_cgp_align_score()
543 l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; in bcf_cgp_align_score()
847 int qbeg, qpos, qend, tbeg, tend, kk; in bcf_call_gap_prep() local
881 0, &tend) - qbeg; in bcf_call_gap_prep()
891 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
919 for (l = 0; l < qend - qbeg; ++l) in bcf_call_gap_prep()
[all …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dbam2bcf_indel.c498 int qbeg, int qend, in bcf_cgp_align_score() argument
519 if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) in bcf_cgp_align_score()
523 for (l = qbeg; l < qend; ++l) { in bcf_cgp_align_score()
529 qq[l - qbeg] = qval; in bcf_cgp_align_score()
535 query, qend - qbeg, qq, &apf, 0, 0); in bcf_cgp_align_score()
543 l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; in bcf_cgp_align_score()
847 int qbeg, qpos, qend, tbeg, tend, kk; in bcf_call_gap_prep() local
881 0, &tend) - qbeg; in bcf_call_gap_prep()
891 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
919 for (l = 0; l < qend - qbeg; ++l) in bcf_call_gap_prep()
[all …]
H A Dbam2bcf_indel.c.pysam.c500 int qbeg, int qend, in bcf_cgp_align_score() argument
521 if (!(qq = (uint8_t*) calloc(qend - qbeg, 1))) in bcf_cgp_align_score()
525 for (l = qbeg; l < qend; ++l) { in bcf_cgp_align_score()
531 qq[l - qbeg] = qval; in bcf_cgp_align_score()
537 query, qend - qbeg, qq, &apf, 0, 0); in bcf_cgp_align_score()
545 l = (int)(100. * sc / (qend - qbeg) + .499) * bca->indel_bias; in bcf_cgp_align_score()
849 int qbeg, qpos, qend, tbeg, tend, kk; in bcf_call_gap_prep() local
883 0, &tend) - qbeg; in bcf_call_gap_prep()
893 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep()
921 for (l = 0; l < qend - qbeg; ++l) in bcf_call_gap_prep()
[all …]
/dports/devel/libconfuse/confuse-3.3/src/
H A Dlexer.l66 static void qbeg(int state);
118 "/*" qbeg(comment);
386 static void qbeg(int state)
433 qbeg(comment);
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/
H A DDfState.java353 IQueryAtom qbeg = (IQueryAtom) qbond.getBegin(); in matchNext() local
356 int begIdx = amap[qbeg.getIndex()]; in matchNext()
383 if (qbond.matches(bond) && feasible(bidx + 1, qbeg, beg)) in matchNext()
392 if (feasible(bidx, qbeg, aiter.next())) in matchNext()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/splign/
H A Dsplign_formatter.cpp303 size_t qbeg = s.m_box[0]; in AsAlignmentText() local
337 if(qbeg < qfin) { in AsAlignmentText()
338 q0 = qbeg; in AsAlignmentText()
343 q1 = qbeg; in AsAlignmentText()
385 MakeLeftHeader(qbeg + 1, &l1); in AsAlignmentText()
472 q0 = qbeg + iq; in AsAlignmentText()
475 q0 = qbeg - iq; in AsAlignmentText()
/dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/gcc/gcc/
H A Dcfgloopmanip.c161 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
184 qbeg = queue; in fix_bb_placements()
186 *qbeg = from; in fix_bb_placements()
188 while (qbeg != qend) in fix_bb_placements()
190 from = *qbeg; in fix_bb_placements()
191 qbeg++; in fix_bb_placements()
192 if (qbeg == qtop) in fix_bb_placements()
193 qbeg = queue; in fix_bb_placements()
/dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/gcc/gcc/
H A Dcfgloopmanip.c161 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
184 qbeg = queue; in fix_bb_placements()
186 *qbeg = from; in fix_bb_placements()
188 while (qbeg != qend) in fix_bb_placements()
190 from = *qbeg; in fix_bb_placements()
191 qbeg++; in fix_bb_placements()
192 if (qbeg == qtop) in fix_bb_placements()
193 qbeg = queue; in fix_bb_placements()
/dports/devel/aarch64-none-elf-gcc/gcc-8.4.0/gcc/
H A Dcfgloopmanip.c184 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
211 qbeg = queue; in fix_bb_placements()
213 *qbeg = from; in fix_bb_placements()
215 while (qbeg != qend) in fix_bb_placements()
218 from = *qbeg; in fix_bb_placements()
219 qbeg++; in fix_bb_placements()
220 if (qbeg == qtop) in fix_bb_placements()
221 qbeg = queue; in fix_bb_placements()
/dports/lang/gcc9/gcc-9.4.0/gcc/
H A Dcfgloopmanip.c184 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
211 qbeg = queue; in fix_bb_placements()
213 *qbeg = from; in fix_bb_placements()
215 while (qbeg != qend) in fix_bb_placements()
218 from = *qbeg; in fix_bb_placements()
219 qbeg++; in fix_bb_placements()
220 if (qbeg == qtop) in fix_bb_placements()
221 qbeg = queue; in fix_bb_placements()
/dports/devel/riscv64-gcc/gcc-8.3.0/gcc/
H A Dcfgloopmanip.c184 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
211 qbeg = queue; in fix_bb_placements()
213 *qbeg = from; in fix_bb_placements()
215 while (qbeg != qend) in fix_bb_placements()
218 from = *qbeg; in fix_bb_placements()
219 qbeg++; in fix_bb_placements()
220 if (qbeg == qtop) in fix_bb_placements()
221 qbeg = queue; in fix_bb_placements()
/dports/lang/gcc12-devel/gcc-12-20211205/gcc/
H A Dcfgloopmanip.c183 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
210 qbeg = queue; in fix_bb_placements()
212 *qbeg = from; in fix_bb_placements()
214 while (qbeg != qend) in fix_bb_placements()
217 from = *qbeg; in fix_bb_placements()
218 qbeg++; in fix_bb_placements()
219 if (qbeg == qtop) in fix_bb_placements()
220 qbeg = queue; in fix_bb_placements()
/dports/devel/riscv32-unknown-elf-gcc/gcc-8.4.0/gcc/
H A Dcfgloopmanip.c184 basic_block *queue, *qtop, *qbeg, *qend; in fix_bb_placements() local
211 qbeg = queue; in fix_bb_placements()
213 *qbeg = from; in fix_bb_placements()
215 while (qbeg != qend) in fix_bb_placements()
218 from = *qbeg; in fix_bb_placements()
219 qbeg++; in fix_bb_placements()
220 if (qbeg == qtop) in fix_bb_placements()
221 qbeg = queue; in fix_bb_placements()

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