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Searched refs:stage3list (Results 1 – 4 of 4) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dgmap.c1380 stage3list = List_push(stage3list,(void *) stage3); in update_stage3list()
1555 stage3list = List_push(stage3list,(void *) stage3); in stage3_from_usersegment()
1951 stage3list = List_push(stage3list,(void *) stage3); in stage3_from_gregions()
2398 stage3list = List_push(stage3list,(void *) stage3); in merge_left_and_right_readthrough()
3090 stage3list = stage3list_remove_duplicates(stage3list); in check_for_local()
3483 stage3list = List_push(stage3list,(void *) new_left); in check_for_chimera()
3508 stage3list = stage3list_remove_duplicates(stage3list); in check_for_chimera()
3815 stage3list = List_append(stage3list,all_middlepieces); in check_middle_piece_local()
4046 stage3list = List_append(stage3list,middlepieces); in check_middle_piece_chimera()
4111 stage3list = stage3list_sort(stage3list); in apply_stage3()
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H A Dstage3.h202 Stage3_compute_mapq (List_T stage3list);
204 Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list);
206 Stage3_recompute_goodness (List_T stage3list);
208 Stage3_recompute_coverage (List_T stage3list, Sequence_T queryseq);
H A Dstage3.c5475 while (stage3list != NULL) { in Stage3_count_paths()
5476 this = (T) List_head(stage3list); in Stage3_count_paths()
5482 stage3list = List_next(stage3list); in Stage3_count_paths()
5492 Stage3_compute_mapq (List_T stage3list) { in Stage3_compute_mapq() argument
5498 if (stage3list != NULL) { in Stage3_compute_mapq()
5500 p = stage3list; in Stage3_compute_mapq()
5514 for (p = stage3list; p != NULL; p = List_next(p)) { in Stage3_compute_mapq()
5520 for (p = stage3list; p != NULL; p = List_next(p)) { in Stage3_compute_mapq()
5550 for (p = stage3list; p != NULL; p = List_next(p)) { in Stage3_recompute_coverage()
6114 for (r = stage3list; r != NULL; r = List_next(r)) {
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/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog617 * gmap.c: Setting npaths_primary and npaths_altloc when stage3list is NULL
1673 Stage3_merge_chimera, and appending middlepieces to stage3list. Changed
2899 Removed all references to a nonjoinable list, and using stage3list as the
12219 * gmap.c: Sorting stage3list before evaluating for chimeras
15449 stage3list
15483 * gmap.c: Not sorting first part of stage3list when chimera is present