| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | univdiag.c | 25 new->univdiagonal = univdiagonal;
68 new->univdiagonal = univdiagonal;
93 T univdiagonal;
97 univdiagonal = (T) List_head(p);
98 FREE(univdiagonal);
148 } else if (x->univdiagonal < y->univdiagonal) { in Univdiag_ascending_cmp()
150 } else if (y->univdiagonal < x->univdiagonal) { in Univdiag_ascending_cmp()
171 } else if (x->univdiagonal > y->univdiagonal) { in Univdiag_descending_cmp()
173 } else if (y->univdiagonal > x->univdiagonal) { in Univdiag_descending_cmp()
187 if (x->univdiagonal < y->univdiagonal) { in Univdiag_diagonal_cmp()
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| H A D | segment-search.c | 501 Univcoord_T *targets, univdiagonal, left; in make_records() local
591 univdiagonal = record->univdiagonal; in make_records()
592 left = univdiagonal - querylength; in make_records()
1121 Univcoord_T univdiagonal; in solve_all() local
1135 univdiagonal = anchor_segment->univdiagonal; in solve_all()
1141 …while (j >= 0 && univdiagonal <= records[j].univdiagonal + overall_max_distance && records[j].chrn… in solve_all()
1147 …while (j < nrecords && records[j].univdiagonal <= univdiagonal + overall_max_distance && records[j… in solve_all()
1154 anchor_segment->univdiagonal,anchor_segment->univdiagonal - anchor_segment->chroffset, in solve_all()
1222 if (segment->univdiagonal + segment->querypos >= univdiagonal + anchor_segment->querypos) { in solve_all()
1289 if (segment->univdiagonal + segment->queryend <= univdiagonal + anchor_segment->queryend) { in solve_all()
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| H A D | extension-search.c | 375 univdiagonal = positions[i] + diagterm; in Elt_read_queryfwd()
460 univdiagonal = positions[i] + diagterm; in Elt_read_queryrev()
538 univdiagonal = this->all_univdiagonals[i];
611 univdiagonal = this->all_univdiagonals[i];
1499 univdiagonal = left_univdiagonal_array[i]->univdiagonal; in process_seed()
1504 while (j < nleft && left_univdiagonal_array[j]->univdiagonal == univdiagonal) { in process_seed()
1533 univdiagonal = right_univdiagonal_array[i]->univdiagonal; in process_seed()
1538 while (j < nright && right_univdiagonal_array[j]->univdiagonal == univdiagonal) { in process_seed()
1628 univdiagonal = queryfwd_univdiagonal; in extend_seeds()
1634 univdiagonal = queryfwd_univdiagonal; in extend_seeds()
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| H A D | univdiagpool.c | 150 Univdiag_new (T this, int qstart, int qend, Univcoord_T univdiagonal) { in Univdiag_new() argument
166 univdiag->univdiagonal = univdiagonal; in Univdiag_new()
171 …debug(printf("Creating %p: %u %d..%d\n",univdiag,univdiag->univdiagonal,univdiag->querystart,univd… in Univdiag_new()
179 Univdiagpool_push (List_T list, T this, int qstart, int qend, Univcoord_T univdiagonal) { in Univdiagpool_push() argument
196 univdiag->univdiagonal = univdiagonal; in Univdiagpool_push()
201 …debug(printf("Creating %p: %u %d..%d\n",univdiag,univdiag->univdiagonal,univdiag->querystart,univd… in Univdiagpool_push()
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| H A D | path-solve.c | 487 Univcoord_T univdiagonal, left, low_left; in attach_qstart_diagonal() local
548 if (low_univdiagonal == univdiagonal) { in attach_qstart_diagonal()
574 nindels = low_univdiagonal - univdiagonal; in attach_qstart_diagonal()
618 nindels = univdiagonal - low_univdiagonal; in attach_qstart_diagonal()
1465 Univcoord_T univdiagonal, left, high_left; in attach_qend_diagonal() local
1536 if (high_univdiagonal == univdiagonal) { in attach_qend_diagonal()
1551 /*left*/univdiagonal - querylength, in attach_qend_diagonal()
3512 if (diagonal->univdiagonal < min_low) { in Path_solve_from_diagonals()
3513 min_low = diagonal->univdiagonal; in Path_solve_from_diagonals()
3556 if (diagonal->univdiagonal > max_high) { in Path_solve_from_diagonals()
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| H A D | univdiagpool.h | 24 Univdiag_new (T this, int qstart, int qend, Univcoord_T univdiagonal);
26 Univdiagpool_push (List_T list, T this, int qstart, int qend, Univcoord_T univdiagonal);
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| H A D | distant-dna.c | 100 Univcoord_T startfrag_genomicstart, endfrag_genomicstart, univdiagonal; in Distant_dna_solve() local
292 univdiagonal = Substring_left(startfrag) + (Univcoord_T) querylength; in Distant_dna_solve()
293 pos5 = (univdiagonal >= (Univcoord_T) querylength) ? 0 : (int) -Substring_left(startfrag); in Distant_dna_solve()
294 …pos3 = (univdiagonal <= genomelength) ? querylength : (int) (genomelength - Substring_left(startfr… in Distant_dna_solve()
297 univdiagonal,pos5,pos3,querylength, in Distant_dna_solve()
309 univdiagonal,pos5,pos3,querylength, in Distant_dna_solve()
477 univdiagonal = Substring_left(startfrag) + (Univcoord_T) querylength; in Distant_dna_solve()
478 pos5 = (univdiagonal >= (Univcoord_T) querylength) ? 0 : (int) -Substring_left(startfrag); in Distant_dna_solve()
479 …pos3 = (univdiagonal <= genomelength) ? querylength : (int) (genomelength - Substring_left(startfr… in Distant_dna_solve()
482 univdiagonal,pos5,pos3,querylength, in Distant_dna_solve()
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| H A D | univdiagdef.h | 17 Univcoord_T univdiagonal; member
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| H A D | record.h | 15 Univcoord_T univdiagonal; /* Primary sort */ member
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| H A D | substring.h | 72 Univcoord_T univdiagonal, int qend, int querylength,
77 Univcoord_T univdiagonal, int pos3, int querylength, bool plusp, int genestrand,
83 Univcoord_T univdiagonal, int qstart, int querylength,
89 Univcoord_T univdiagonal, int pos5, int querylength, bool plusp, int genestrand,
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| H A D | univdiag.h | 16 Univdiag_new (int qstart, int qend, Univcoord_T univdiagonal);
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| H A D | diag.h | 16 Diag_new (int querystart, int queryend, Univcoord_T univdiagonal);
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| H A D | kmer-search.c | 5491 univdiagonal = univdiagonal1; in combine_ends_plus()
5522 univdiagonal = univdiagonal0; in combine_ends_plus()
5575 univdiagonal = univdiagonal1; in combine_ends_plus()
5606 univdiagonal = univdiagonal0; in combine_ends_plus()
5661 univdiagonal = univdiagonal1; in combine_ends_plus()
5693 univdiagonal = univdiagonal0; in combine_ends_plus()
6022 univdiagonal = univdiagonal0; in combine_ends_minus()
6054 univdiagonal = univdiagonal1; in combine_ends_minus()
6107 univdiagonal = univdiagonal0; in combine_ends_minus()
6139 univdiagonal = univdiagonal1; in combine_ends_minus()
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| H A D | indel.c | 684 Univcoord_T univdiagonal; in Indel_resolve_middle_deletion_or_splice() local
725 univdiagonal = left + (Univcoord_T) querylength; in Indel_resolve_middle_deletion_or_splice()
726 …queryend = (univdiagonal + queryend <= genomelength + querylength) ? queryend : (int) (genomelengt… in Indel_resolve_middle_deletion_or_splice()
733 univdiagonal = left + (Univcoord_T) querylength; in Indel_resolve_middle_deletion_or_splice()
734 …queryend = (univdiagonal + queryend <= genomelength + querylength) ? queryend : (int) (genomelengt… in Indel_resolve_middle_deletion_or_splice()
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| H A D | substring.c | 1166 Univcoord_T univdiagonal; in Substring_trim_qstart_nosplice() local
1323 Univcoord_T univdiagonal, int qend, int querylength, in Substring_trimmed_qstarts() argument
1333 univdiagonal-chroffset,0,qend,plusp,sensedir)); in Substring_trimmed_qstarts()
1335 left = univdiagonal - (Univcoord_T) querylength; in Substring_trimmed_qstarts()
1402 univdiagonal,pos3,plusp,sensedir)); in Substring_qstart_trim()
1404 left = univdiagonal - (Univcoord_T) querylength; in Substring_qstart_trim()
1475 Univcoord_T univdiagonal, int qstart, int querylength, in Substring_trimmed_qends() argument
1484 univdiagonal-chroffset,qstart,querylength,plusp,sensedir)); in Substring_trimmed_qends()
1486 left = univdiagonal - (Univcoord_T) querylength; in Substring_trimmed_qends()
1552 univdiagonal,pos5,plusp,sensedir)); in Substring_qend_trim()
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| H A D | stage3hr.c | 3973 Univcoord_T univdiagonal, left; in Stage3end_nmatches_substrings() local
4057 univdiagonal = Univcoordlist_head(q); in Stage3end_nmatches_substrings()
4060 qstart,qend,univdiagonal,univdiagonal - chroffset)); in Stage3end_nmatches_substrings()
4159 univdiagonal = Univcoordlist_head(q); in Stage3end_nmatches_substrings()
4162 qstart,qend,univdiagonal,univdiagonal - chroffset)); in Stage3end_nmatches_substrings()
4319 Univcoord_T univdiagonal, left; in Stage3end_new_substrings() local
4399 univdiagonal = Univcoordlist_head(q); in Stage3end_new_substrings()
4402 qstart,qend,univdiagonal,univdiagonal - chroffset)); in Stage3end_new_substrings()
4505 univdiagonal = Univcoordlist_head(q); in Stage3end_new_substrings()
4508 qstart,qend,univdiagonal,univdiagonal - chroffset)); in Stage3end_new_substrings()
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| H A D | stage3hr.h | 333 Univcoord_T univdiagonal, int pos5, int pos3, int querylength,
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| H A D | concordance.c | 1801 path_start_x = diagonalx->univdiagonal;
1802 path_start_y = diagonaly->univdiagonal;
1811 path_end_x = diagonalx->univdiagonal;
1812 path_end_y = diagonaly->univdiagonal;
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| H A D | genome.c | 10701 Univcoord_T univdiagonal; in Genome_fill_buffer_simple() local
10724 univdiagonal = left + length; in Genome_fill_buffer_simple()
10725 pos5 = (univdiagonal >= (Univcoord_T) length) ? 0 : (int) -left; in Genome_fill_buffer_simple()
10726 pos3 = (univdiagonal <= genomelength) ? (int) length : (int) (genomelength - left); in Genome_fill_buffer_simple()
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| H A D | regiondb.c | 986 diagonal = middle_diagonals[i]->univdiagonal;
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 1200 univdiagonal, qstart, and qend, instead of a Univdiag_T object
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