/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/ |
H A D | strsearch.hpp | 301 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/ |
H A D | strsearch.hpp | 301 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 …]
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/dports/biology/bwa/bwa-0.7.17/ |
H A D | bwtsw2_chain.c | 10 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()
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H A D | bwamem.c | 170 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 …]
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
H A D | blast2sam.pl | 13 my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq); 33 @cigar = (); $qbeg = 0; 39 unless ($qbeg) { 40 $qbeg = $1;
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
H A D | bam2bcf_indel.c | 274 int qbeg, qend, tbeg, tend, sc; in bcf_call_gap_prep() local 285 for (l = qbeg; l < qend; ++l) in bcf_call_gap_prep() 286 query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)]; in bcf_call_gap_prep() 290 qq = calloc(qend - qbeg, 1); in bcf_call_gap_prep() 293 for (l = qbeg; l < qend; ++l) { in bcf_call_gap_prep() 294 qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; in bcf_call_gap_prep() 295 if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; in bcf_call_gap_prep() 296 if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; in bcf_call_gap_prep() 299 (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0); in bcf_call_gap_prep() 305 (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0); in bcf_call_gap_prep() [all …]
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | blast2sam.pl | 38 my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq); 65 @cigar = (); $qbeg = 0; 71 unless ($qbeg) { 72 $qbeg = $1;
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/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
H A D | bam2bcf_indel.c | 327 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 …]
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam2bcf_indel.c | 388 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 …]
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H A D | bam2bcf_indel.c.pysam.c | 390 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 …]
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam2bcf_indel.c | 388 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 …]
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | bam2bcf_indel.c | 498 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 …]
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | bam2bcf_indel.c | 498 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 …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | bam2bcf_indel.c | 498 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 …]
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H A D | bam2bcf_indel.c.pysam.c | 500 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 …]
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/dports/devel/libconfuse/confuse-3.3/src/ |
H A D | lexer.l | 66 static void qbeg(int state); 118 "/*" qbeg(comment); 386 static void qbeg(int state) 433 qbeg(comment);
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ |
H A D | DfState.java | 353 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/splign/ |
H A D | splign_formatter.cpp | 303 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()
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/dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/gcc/gcc/ |
H A D | cfgloopmanip.c | 161 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()
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/dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/gcc/gcc/ |
H A D | cfgloopmanip.c | 161 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()
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/dports/devel/aarch64-none-elf-gcc/gcc-8.4.0/gcc/ |
H A D | cfgloopmanip.c | 184 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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/dports/lang/gcc9/gcc-9.4.0/gcc/ |
H A D | cfgloopmanip.c | 184 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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/dports/devel/riscv64-gcc/gcc-8.3.0/gcc/ |
H A D | cfgloopmanip.c | 184 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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/dports/lang/gcc12-devel/gcc-12-20211205/gcc/ |
H A D | cfgloopmanip.c | 183 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()
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/dports/devel/riscv32-unknown-elf-gcc/gcc-8.4.0/gcc/ |
H A D | cfgloopmanip.c | 184 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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