| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | dynprog_end.h | 31 int extraband_end, double defect_rate, Endalign_T endalign,
42 int extraband_end, double defect_rate, int contlength);
51 int extraband_end, double defect_rate, Endalign_T endalign,
62 int extraband_end, double defect_rate, int contlength);
99 Pairpool_T pairpool, int extraband_end, double defect_rate);
115 Pairpool_T pairpool, int extraband_end, double defect_rate);
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| H A D | splicetrie.c | 179 Pairpool_T pairpool, int extraband_end, double defect_rate) { in solve_end5_aux() argument
212 extraband_end,defect_rate,contlength)) != NULL) { in solve_end5_aux()
308 extraband_end,defect_rate,contlength)) != NULL) { in solve_end5_aux()
397 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in solve_end5_aux()
459 Pairpool_T pairpool, int extraband_end, double defect_rate) { in solve_end3_aux() argument
491 extraband_end,defect_rate,contlength)) != NULL) { in solve_end3_aux()
584 extraband_end,defect_rate,contlength)) != NULL) { in solve_end3_aux()
732 Pairpool_T pairpool, int extraband_end, double defect_rate) { in Splicetrie_solve_end5() argument
759 cdna_direction,watsonp,genestrand,jump_late_p,pairpool,extraband_end,defect_rate); in Splicetrie_solve_end5()
799 Pairpool_T pairpool, int extraband_end, double defect_rate) { in Splicetrie_solve_end3() argument
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| H A D | splicetrie.h | 46 Pairpool_T pairpool, int extraband_end, double defect_rate);
65 Pairpool_T pairpool, int extraband_end, double defect_rate);
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| H A D | dynprog_end.c | 1277 int extraband_end, double defect_rate, Endalign_T endalign, in Dynprog_end5_gap() argument
1629 int extraband_end, double defect_rate, int contlength) { in Dynprog_end5_splicejunction() argument
1891 int extraband_end, double defect_rate, Endalign_T endalign, in Dynprog_end3_gap() argument
2206 int extraband_end, double defect_rate, int contlength) { in Dynprog_end3_splicejunction() argument
2750 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS, in Dynprog_end5_known()
2864 pairpool,extraband_end,defect_rate); in Dynprog_end5_known()
2882 pairpool,extraband_end,defect_rate); in Dynprog_end5_known()
3010 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS, in Dynprog_end3_known()
3124 pairpool,extraband_end,defect_rate); in Dynprog_end3_known()
3142 pairpool,extraband_end,defect_rate); in Dynprog_end3_known()
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| H A D | stage3.h | 403 int extramaterial_end, int extraband_end);
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| H A D | stage3.c | 342 static int extraband_end; variable
403 extraband_end = extraband_end_in; in Stage3_setup()
4149 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS,/*require_pos_score_p*/true); in trim_end5_indels()
4441 extraband_end,defect_rate,/*endalign*/QUERYEND_INDELS,/*require_pos_score_p*/false); in trim_end5_exons()
4635 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS,/*require_pos_score_p*/true); in trim_end3_indels()
10253 extraband_end,defect_rate,/*endalign*/QUERYEND_INDELS,/*require_pos_score_p*/false); in distalmedial_ending5()
10355 extraband_end,defect_rate); in extend_ending5()
10366 extraband_end,defect_rate,endalign,/*require_pos_score_p*/false); in extend_ending5()
10477 extraband_end,defect_rate,/*endalign*/QUERYEND_INDELS, in distalmedial_ending3()
10578 extraband_end,defect_rate); in extend_ending3()
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| H A D | gsnap.c | 177 static int extraband_end = 3; /* Shouldn't differ from 0, since onesidegapp is true? */
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| H A D | gmap.c | 289 static int extraband_end = 6; /* Was 6. Shouldn't differ from 0, since onesidegapp is true? variable
7030 extraband_single,extraband_end,extraband_paired, in main()
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| /dports/biology/gmap/gmap-2020-09-12/ |
| H A D | ChangeLog | 21710 * gmap.c: Reduced extraband_end
25672 * gmap.c, snap.c: Created separate parameters for extraband_end and
25677 extraband_end and extraband_paired. Renamed maxlookback to nullgap.
25680 * dynprog.h: Created separate parameters for extraband_end and
25683 * dynprog.c: Created separate parameters for extraband_end and
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