mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
113 lines
2.9 KiB
C++
113 lines
2.9 KiB
C++
#include "htab.h"
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#include "ksort.h"
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#include "Hash_Table.h"
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typedef struct { // this struct is not strictly necessary; we can use k_mer_pos instead, with modifications
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uint64_t srt;
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uint32_t self_off;
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uint32_t other_off;
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} anchor1_t;
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#define an_key1(a) ((a).srt)
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#define an_key2(a) ((a).self_off)
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KRADIX_SORT_INIT(ha_an1, anchor1_t, an_key1, 8)
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KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
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typedef struct {
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int n;
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const ha_idxpos_t *a;
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} seed1_t;
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struct ha_abuf_s {
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uint64_t n_a, m_a;
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uint32_t old_mz_m;
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ha_mz1_v mz;
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seed1_t *seed;
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anchor1_t *a;
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};
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ha_abuf_t *ha_abuf_init(void)
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{
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return (ha_abuf_t*)calloc(1, sizeof(ha_abuf_t));
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}
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void ha_abuf_destroy(ha_abuf_t *ab)
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{
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free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);
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}
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void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain)
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{
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extern void *ha_flt_tab;
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extern ha_pt_t *ha_idx;
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uint32_t i;
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uint64_t k, l;
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// prepare
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clear_Candidates_list(cl);
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clear_overlap_region_alloc(overlap_list);
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recover_UC_Read(ucr, &R_INF, rid);
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ab->mz.n = 0, ab->n_a = 0;
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// get the list of anchors
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ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !asm_opt.no_HPC, &ab->mz, ha_flt_tab);
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if (ab->mz.m > ab->old_mz_m) {
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ab->old_mz_m = ab->mz.m;
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REALLOC(ab->seed, ab->old_mz_m);
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}
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for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
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ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &ab->seed[i].n);
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ab->n_a += ab->seed[i].n;
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}
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if (ab->n_a > ab->m_a) {
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ab->m_a = ab->n_a;
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ab->m_a = ab->m_a > 16? ab->m_a + (ab->m_a>>1) : 16;
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REALLOC(ab->a, ab->m_a);
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}
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for (i = 0, k = 0; i < ab->mz.n; ++i) {
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int j;
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ha_mz1_t *z = &ab->mz.a[i];
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seed1_t *s = &ab->seed[i];
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for (j = 0; j < s->n; ++j) {
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const ha_idxpos_t *y = &s->a[j];
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anchor1_t *an = &ab->a[k++];
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uint8_t rev;
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if (z->rev == y->rev) { // forward strand
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rev = 0;
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an->self_off = z->pos;
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an->other_off = y->pos;
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} else { // reverse strand
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rev = 1;
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an->self_off = ucr->length - 1 - (z->pos + 1 - z->span);
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an->other_off = R_INF.read_length[y->rid] - 1 - (y->pos + 1 - y->span);
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}
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an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
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}
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}
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// sort anchors
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radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
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for (k = 1, l = 0; k <= ab->n_a; ++k) {
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if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
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if (k - l > 1)
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radix_sort_ha_an2(ab->a + l, ab->a + k);
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l = k;
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}
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}
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// copy over to _cl_
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if (ab->m_a >= (uint64_t)cl->size) {
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cl->size = ab->m_a;
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REALLOC(cl->list, cl->size);
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}
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for (k = 0; k < ab->n_a; ++k) {
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cl->list[k].readID = ab->a[k].srt >> 33;
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cl->list[k].strand = ab->a[k].srt >> 32 & 1;
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cl->list[k].offset = ab->a[k].other_off;
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cl->list[k].self_offset = ab->a[k].self_off;
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}
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cl->length = ab->n_a;
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calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, band_width_threshold, keep_whole_chain);
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}
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