| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | intron.c | 21 int cdna_direction
47 } else if (cdna_direction > 0) {
50 cdna_direction,watsonp,chroffset+leftgenomepos,chroffset+leftgenomepos+1U));
60 cdna_direction,watsonp,chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U));
69 } else if (cdna_direction < 0) {
72 cdna_direction,watsonp,chroffset+leftgenomepos,chroffset+leftgenomepos+1U));
82 cdna_direction,watsonp,chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U));
112 } else if (cdna_direction > 0) {
130 } else if (cdna_direction < 0) {
158 } else if (cdna_direction > 0) {
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| H A D | pair.h | 105 bool watsonp, int cdna_direction,
148 bool watsonp, int cdna_direction, bool genomefirstp, int invertmode);
164 int qindels, int tindels, int unknowns, bool watsonp, int cdna_direction,
246 bool watsonp, int cdna_direction);
268 int chimera_cdna_direction, char *strain, int cdna_direction);
304 double *min_splice_prob, List_T pairs, int cdna_direction);
308 double *min_splice_prob, struct T *ptr, int npairs, int cdna_direction);
313 Pair_frac_error (List_T pairs, int cdna_direction);
320 int cdna_direction, int minpos, int maxpos);
355 Pair_start_bound (int *cdna_direction, List_T pairs, int breakpoint);
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| H A D | dynprog_genome.c | 344 if (cdna_direction > 0) { in get_splicesite_probs()
357 if (cdna_direction > 0) { in get_splicesite_probs()
375 if (cdna_direction > 0) { in get_splicesite_probs()
387 if (cdna_direction > 0) { in get_splicesite_probs()
894 if (cdna_direction > 0) { in bridge_intron_gap_8_site_level()
974 if (cdna_direction > 0) { in bridge_intron_gap_8_site_level()
1018 if (cdna_direction > 0) { in bridge_intron_gap_8_site_level()
1469 cdna_direction,watsonp); in bridge_intron_gap_8_ud()
1767 if (cdna_direction > 0) { in bridge_intron_gap_16_site_level()
2488 if (cdna_direction > 0) { in bridge_intron_gap_site_level()
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| H A D | stage3.c | 575 int cdna_direction; member
1841 cdna_direction); in assign_gap_types()
2107 cdna_direction); in assign_intron_probs()
2470 cdna_direction); in add_dualbreak()
5104 cdna_direction); in fill_in_gaps()
5320 this_left->cdna_direction = cdna_direction; in make_pairarray_merge()
5968 new->cdna_direction = cdna_direction; in Stage3_new()
5978 new->cdna_direction = cdna_direction; in Stage3_new()
6150 new->cdna_direction = old->cdna_direction;
9416 cdna_direction); in traverse_genome_gap()
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| H A D | pair.c | 2908 feature_strand = watsonp ? cdna_direction : -cdna_direction; in print_gff3_est_match()
2932 target_strand = cdna_direction != 0 ? cdna_direction : (watsonp ? 1 : -1); in print_gff3_est_match()
3756 cdna_direction); in Pair_print_gff3()
3770 cdna_direction); in Pair_print_gff3()
3934 cdna_direction = -cdna_direction; in Pair_print_bedpe()
9869 cdna_direction += 1; in Pair_cdna_direction()
9871 cdna_direction -= 1; in Pair_cdna_direction()
9895 *cdna_direction = 0; in Pair_start_bound()
9933 *cdna_direction = +1; in Pair_start_bound()
9935 *cdna_direction = -1; in Pair_start_bound()
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| H A D | dynprog_single.h | 37 int roffset, int goffsetL, int rev_goffsetR, int cdna_direction,
46 int length1, int length2, int revoffset1, int revoffset2, int cdna_direction,
54 int length1, int length2, int offset1, int offset2, int cdna_direction,
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| H A D | splicetrie.c | 178 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in solve_end5_aux() argument
397 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end5_aux()
409 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end5_aux()
421 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end5_aux()
433 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end5_aux()
458 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in solve_end3_aux() argument
671 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end3_aux()
731 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in Splicetrie_solve_end5() argument
759 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in Splicetrie_solve_end5()
798 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in Splicetrie_solve_end3() argument
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| H A D | splicetrie.h | 45 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p,
64 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p,
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| H A D | dynprog_single.c | 893 int roffset, int goffsetL, int rev_goffsetR, int cdna_direction, in Dynprog_microexon_int() argument
936 if (cdna_direction > 0) { in Dynprog_microexon_int()
943 } else if (cdna_direction < 0) { in Dynprog_microexon_int()
1105 if (cdna_direction > 0) { in Dynprog_microexon_int()
1117 if (cdna_direction > 0) { in Dynprog_microexon_int()
1211 int rlength, int glength, int rev_roffset, int rev_goffset, int cdna_direction,
1228 if (cdna_direction > 0) {
1235 } else if (cdna_direction < 0) {
1327 int rlength, int glength, int roffset, int goffset, int cdna_direction,
1344 if (cdna_direction > 0) {
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| H A D | dynprog_end.h | 98 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p,
114 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p,
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| H A D | dynprog_genome.h | 30 int cdna_direction, bool watsonp, int genestrand,
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| H A D | stage3.h | 296 int cdna_direction, int sensedir,
304 Stage3_new_from_pairs (List_T pairs, int cdna_direction, bool watsonp, int genestrand, int sensedir,
332 Stage3_compute_ends (int *cdna_direction, int *sensedir, List_T *finalpairs1, int *npairs1, int *go…
360 Stage3_compute_one (int *cdna_direction, int *sensedir,
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| H A D | chimera.c | 66 int cdna_direction; member
105 return this->cdna_direction; in Chimera_cdna_direction()
115 if (this->cdna_direction >= 0) { in Chimera_print_sam_tag()
179 int exonexonpos, int cdna_direction, in Chimera_new() argument
191 new->cdna_direction = cdna_direction; in Chimera_new()
215 if (this->cdna_direction > 0) { in Chimera_print()
217 } else if (this->cdna_direction < 0) { in Chimera_print()
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| H A D | intron.h | 41 int cdna_direction
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| H A D | chimera.h | 36 int exonexonpos, int cdna_direction,
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| H A D | dynprog_end.c | 2698 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in Dynprog_end5_known() argument
2788 if (cdna_direction > 0) { in Dynprog_end5_known()
2803 if (cdna_direction > 0) { in Dynprog_end5_known()
2863 cdna_direction,watsonp,genestrand,jump_late_p, in Dynprog_end5_known()
2881 cdna_direction,watsonp,genestrand,jump_late_p, in Dynprog_end5_known()
2957 int cdna_direction, bool watsonp, int genestrand, bool jump_late_p, in Dynprog_end3_known() argument
3048 if (cdna_direction > 0) { in Dynprog_end3_known()
3063 if (cdna_direction > 0) { in Dynprog_end3_known()
3123 cdna_direction,watsonp,genestrand,jump_late_p, in Dynprog_end3_known()
3141 cdna_direction,watsonp,genestrand,jump_late_p, in Dynprog_end3_known()
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| H A D | gmap.c | 1275 int npairs, cdna_direction, matches, unknowns, mismatches, qopens, qindels, topens, tindels, in update_stage3list() local
1339 pairarray = Stage3_compute_one(&cdna_direction,&sensedir,&pairs,&npairs,&goodness, in update_stage3list()
1371 } else if ((stage3 = Stage3_new(pairarray,pairs,npairs,goodness,cdna_direction,sensedir, in update_stage3list()
1516 pairarray = Stage3_compute_ends(&cdna_direction,&sensedir,&pairs,&npairs,&goodness, in stage3_from_usersegment()
1912 pairarray = Stage3_compute_ends(&cdna_direction,&sensedir,&pairs,&npairs,&goodness, in stage3_from_gregions()
1942 } else if ((stage3 = Stage3_new(pairarray,pairs,npairs,goodness,cdna_direction,sensedir, in stage3_from_gregions()
2604 *cdna_direction = 0; in find_breakpoint()
2637 *cdna_direction = try_cdna_direction; in find_breakpoint()
2644 *cdna_direction = found_cdna_direction; in find_breakpoint()
4074 int cdna_direction, genestrand, sensedir; in apply_stage3() local
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| H A D | pairpool.c | 1139 cdna_direction); in Pairpool_add_genomeskip()
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 5098 cdna_direction to those for sensedir.
7523 recomputing to find the best cdna_direction.
9769 guess of cdna_direction in Stage3_merge_local_splice.
10249 * stage3.c: Handling PMAP case for final guess at cdna_direction
11324 * stage3.c: Disallowing cdna_direction to be set to 0
11959 * pair.c, pair.h: Taking cdna_direction as a parameter in
22921 cdna_direction information on single gaps.
22923 * stage3.c: Forcing single gaps to be solved. Adding cdna_direction
22979 * intron.c, intron.h: Using cdna_direction information in assigning
27571 * pair.c: Improved consistency check to work when cdna_direction is
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