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Searched refs:QUERYEND_NOGAPS (Results 1 – 5 of 5) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddynprog.h25 typedef enum {QUERYEND_GAP, QUERYEND_INDELS, QUERYEND_NOGAPS, BEST_LOCAL} Endalign_T; enumerator
H A Ddynprog_end.c1326 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end5_gap()
1344 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end5_gap()
1507 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end5_gap()
1530 if (endalign == QUERYEND_NOGAPS) { in Dynprog_end5_gap()
1939 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end3_gap()
1950 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end3_gap()
2092 } else if (endalign == QUERYEND_NOGAPS) { in Dynprog_end3_gap()
2114 if (endalign == QUERYEND_NOGAPS) { in Dynprog_end3_gap()
2750 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS, in Dynprog_end5_known()
3010 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS, in Dynprog_end3_known()
H A Dstage3.c4149 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS,/*require_pos_score_p*/true); in trim_end5_indels()
4635 extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS,/*require_pos_score_p*/true); in trim_end3_indels()
10317 if (endalign == QUERYEND_NOGAPS) { in extend_ending5()
10543 if (endalign == QUERYEND_NOGAPS) { in extend_ending3()
14014 /*extendp*/true,/*endalign*/QUERYEND_NOGAPS,/*forcep*/false); in path_compute_end5()
14145 /*endalign*/QUERYEND_NOGAPS,/*forcep*/false); in path_compute_end3()
14161 /*extendp*/true,/*endalign*/QUERYEND_NOGAPS,/*forcep*/false); in path_compute_end3()
15613 /*extendp*/true,/*endalign*/QUERYEND_NOGAPS,/*forcep*/false); in path_trim()
15638 /*extendp*/true,/*endalign*/QUERYEND_NOGAPS,/*forcep*/false); in path_trim()
17682 /*extendp*/true,/*endalign*/QUERYEND_NOGAPS,/*forcep*/true); in Stage3_merge_chimera()
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H A Ddynprog.c109 case QUERYEND_NOGAPS: return "queryend_nogaps"; in Dynprog_endalign_string()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog3283 when endalign is QUERYEND_NOGAPS
10573 * stage3.c: Using QUERYEND_NOGAPS for pass 9a and pass 9b for GSNAP, so
10599 * stage3.c: Changed endalign for pass 9a and 9b from QUERYEND_NOGAPS to
10942 QUERYEND_NOGAPS instead, to reduce time spent in dynamic programming
11751 * stage3.c: For GMAP, using QUERYEND_INDELS instead of QUERYEND_NOGAPS
11831 QUERYEND_NOGAPS.
11846 BEST_LOCAL, QUERYEND_INDELS, and QUERYEND_NOGAPS. For extensions to