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phasing speedup

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chhylp123
2026-04-11 22:33:18 -04:00
parent 815d709fb9
commit ba8627fb23
13 changed files with 1055 additions and 186 deletions
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anchor.cpp
+25
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@@ -2674,6 +2674,31 @@ void ul_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t
lchain_qgen_mcopy(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off, mcopy_rate, chain_cutoff, mcopy_khit_cut, sp);
}
void p_ec_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, ul_idx_t *uref, overlap_region_alloc *ol, Candidates_list *cl, double bw_thres,
int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t mcopy_num, double mcopy_rate, uint32_t mcopy_khit_cut)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
minimizers_qgen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ);
uint64_t k, l, m, cn = cl->length, yid;
clear_overlap_region_alloc(ol);
for (l = 0, k = 1, m = 0; k <= cn; k++) {
if((k == cn) || (cl->list[k].readID != cl->list[l].readID)) {
if(cl->list[l].readID != rid) {
yid = cl->list[l].readID;
m += lchain_qdp_mcopy_fast(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres,
rid, rl, uref->ug->u.a[yid].len, quick_check, apend_be, gen_off, mcopy_num, mcopy_rate, mcopy_khit_cut, 1);
}
l = k;
}
}
cl->length = m;
}
void h_ec_lchain(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t mcopy_num, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut, uint64_t ocv_w, uint8_t is_raw_chain)
{