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Searched refs:hitpairs (Results 1 – 7 of 7) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dstage1hr.c1967 return hitpairs; in paired_read_segment_search()
2118 return hitpairs; in paired_read_segment_search()
2216 return hitpairs; in paired_read_segment_search()
2241 List_T hitpairs; in paired_read() local
2253 hitpairs = (List_T) NULL; in paired_read()
2344 if (hitpairs == NULL) { in paired_read()
2354 … hitpairs = paired_read_segment_search(&(*abort_pairing_p),&(*samechr),&(*conc_transloc),hitpairs, in paired_read()
2385 return hitpairs; in paired_read()
2417 hitpairs,samechr,conc_transloc); in consolidate_paired_results()
2497 Hitlist_free(&hitpairs); in consolidate_paired_results()
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H A Dconcordance.c204 *hitpairs = Hitlist_push(*hitpairs,hitlistpool,(void *) stage3pair);
303 *hitpairs = Hitlist_push(*hitpairs,hitlistpool,(void *) stage3pair);
420 return hitpairs;
805 &hitpairs,&(*distant_hitpairs), in Concordance_pair_up_genome()
840 &hitpairs,&(*distant_hitpairs), in Concordance_pair_up_genome()
877 &hitpairs,&(*distant_hitpairs), in Concordance_pair_up_genome()
913 &hitpairs,&(*distant_hitpairs), in Concordance_pair_up_genome()
959 return hitpairs; in Concordance_pair_up_genome()
1095 *hitpairs = Hitlist_push(*hitpairs,hitlistpool,(void *) stage3pair); in do_distant_plus_plus()
1245 *hitpairs = Hitlist_push(*hitpairs,hitlistpool,(void *) stage3pair); in do_distant_minus_minus()
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H A Dconcordance.h23 List_T *distant_hitpairs, List_T hitpairs,
41 List_T *samechr, List_T *conc_transloc, List_T hitpairs,
H A Dstage3hr.h283 Stage3pair_concordantp (List_T hitpairs);
285 Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs);
288 Stage3pair_filter_nonconcordant (List_T hitpairs, Hitlistpool_T hitlistpool);
462 Stage3pair_resolve_multimapping (List_T hitpairs, Hitlistpool_T hitlistpool);
H A Dstage3hr.c1718 hitpairs = List_next(hitpairs); in Stage3pair_count_hits()
12404 while (j < n && hitpair_equal(hitpairs[j],hitpairs[i]) == true) {
12422 FREEA(hitpairs);
12425 FREE(hitpairs);
13153 FREEA(hitpairs); in pair_remove_overlaps()
13157 FREE(hitpairs); in pair_remove_overlaps()
13435 FREE(hitpairs); in Stage3pair_remove_overlaps()
13544 FREE(hitpairs); in Stage3pair_remove_overlaps()
13620 FREE(hitpairs); in Stage3pair_remove_overlaps()
14529 FREE(hitpairs);
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/dports/biology/wise/wise2.4.1/src/models/
H A Dhsp2aln_sw.dy301 fprintf(ofp," -hsp2hit_hitaln [no] number of hitpairs to assess\n");
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog3313 translocations compared with other hitpairs
10527 * stage1hr.c, stage3hr.c, stage3hr.h: Added a category of hitpairs called
14209 tally ahead of score in ranking subsumed hitpairs.
14252 cluster. Using hittype to rank hitpairs in hitpair_equal_cmp, but not for
14253 distinguishing hitpairs in hitpair_equal_no_hittype_cmp.
14258 hitpair_position_cmp), both for sorting and for recognizing equal hitpairs.