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r176: enabled the minimap2 chaining heuristic

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Heng Li
2020-04-01 22:06:14 -04:00
parent e75b93ae12
commit b7e5d1c4d3
5 changed files with 44 additions and 65 deletions
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anchor.cpp
+1 -9
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@@ -62,7 +62,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
if (ab->n_a > ab->m_a) {
ab->m_a = ab->n_a;
ab->m_a = ab->m_a > 16? ab->m_a + (ab->m_a>>1) : 16;
kroundup64(ab->m_a);
REALLOC(ab->a, ab->m_a);
}
for (i = 0, k = 0; i < ab->mz.n; ++i) {
@@ -104,12 +104,4 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, band_width_threshold, keep_whole_chain);
#if 0
fprintf(stderr, "B\t%ld\t%ld\n", (long)overlap_list->length, (long)overlap_list->mapped_overlaps_length);
for (int i = 0; i < (int)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->list[i];
fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
(int)r->y_id, (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, r->is_match);
}
#endif
}