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freeze-r304

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chhylp123
2020-08-23 23:34:36 -04:00
parent 03cf0d475c
commit 724990cbe7
7 changed files with 235 additions and 74 deletions
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Assembly.cpp
+17 -14
View File
@@ -12,7 +12,7 @@
#include "kthread.h"
void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf);
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar);
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
All_reads R_INF;
@@ -457,6 +457,7 @@ typedef struct {
kvec_t_u32_warp b_buf;
kvec_t_u64_warp r_buf;
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
@@ -469,6 +470,7 @@ ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
init_Candidates_list(&b->clist);
init_overlap_region_alloc(&b->olist);
init_overlap_region_alloc(&b->olist_hp);
init_fake_cigar(&(b->tmp_region.f_cigar));
kv_init(b->b_buf.a);
kv_init(b->r_buf.a);
kv_init(b->k_flag.a);
@@ -492,6 +494,7 @@ void ha_ovec_destroy(ha_ovec_buf_t *b)
destory_overlap_region_alloc(&b->olist);
destory_overlap_region_alloc(&b->olist_hp);
ha_abuf_destroy(b->ab);
destory_fake_cigar(&(b->tmp_region.f_cigar));
kv_destroy(b->b_buf.a);
kv_destroy(b->r_buf.a);
kv_destroy(b->k_flag.a);
@@ -558,7 +561,7 @@ static void worker_ovec(void *data, long i, int tid)
int fully_cov, abnormal;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -581,10 +584,10 @@ static void worker_ovec(void *data, long i, int tid)
R_INF.paf[i].is_abnormal = abnormal;
R_INF.trio_flag[i] = AMBIGU;
if(ha_idx_hp == NULL)
{
R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &b->b_buf, &b->r_buf, &(b->k_flag), RESEED_HP_RATE, NULL);
}
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), NULL);
// }
if (R_INF.trio_flag[i] != AMBIGU || b->save_ov) {
int is_rev = (asm_opt.number_of_round % 2 == 0);
@@ -615,7 +618,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
int fully_cov, abnormal;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -679,10 +682,10 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
}
R_INF.trio_flag[i] = AMBIGU;
if(ha_idx_hp == NULL)
{
R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &b->b_buf, &b->r_buf, &(b->k_flag), RESEED_HP_RATE, R_INF_FLAG.fp);
}
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), R_INF_FLAG.fp);
// }
fprintf(R_INF_FLAG.fp, "R_INF.trio_flag[%ld]: %u\n", i, R_INF.trio_flag[i]);
@@ -891,7 +894,7 @@ void ha_overlap_and_correct(int round)
free(e[i].second_round_read);
}
free(e);
debug_print_pob_regions();
///debug_print_pob_regions();
}
@@ -1291,7 +1294,7 @@ static void worker_ov_final(void *data, long i, int tid)
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist, 0.001,
asm_opt.max_n_chain, 0, &(b->k_flag), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
asm_opt.max_n_chain, 0, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
overlap_region_sort_y_id(b->olist.list, b->olist.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);
@@ -1357,7 +1360,7 @@ static void worker_ov_final_high_het(void *data, long i, int tid)
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist, HIGH_HET_ERROR_RATE,
asm_opt.max_n_chain, 1, &(b->k_flag), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
overlap_region_sort_y_id(b->olist.list, b->olist.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);
Correct.cpp
+82 -12
View File
@@ -12,6 +12,8 @@
#define generic_key(x) (x)
KRADIX_SORT_INIT(b32, uint32_t, generic_key, 4)
int ha_ov_type(const overlap_region *r, uint32_t len);
void clear_Round2_alignment(Round2_alignment* h)
{
@@ -7268,12 +7270,15 @@ kvec_t_u32_warp* b, kvec_t_u64_warp* r, int min_dp, int min_len)
}
}
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u32_warp* b, kvec_t_u64_warp* r, kvec_t_u8_warp* k_flag, float hp_rate, FILE* fp)
int collect_hp_regions_back(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u32_warp* b, kvec_t_u64_warp* r, kvec_t_u8_warp* k_flag, float hp_rate, FILE* fp)
{
int i, k, qs, qe, ava_k_mer = 0, hp_k_mer = 0;
int min_dp = RESEED_DP;
int i, k, qs, qe, ava_k_mer = 0, hp_k_mer = 0, min_dp;
// min_dp = RESEED_DP;
// if(asm_opt.hom_cov > 0) min_dp = asm_opt.hom_cov * RESEED_PEAK_RATE;
// if(min_dp > RESEED_DP) min_dp = RESEED_DP;
min_dp = RESEED_DP;
if(asm_opt.hom_cov > 0) min_dp = asm_opt.hom_cov * RESEED_PEAK_RATE;
if(min_dp > RESEED_DP) min_dp = RESEED_DP;
if(asm_opt.het_cov > 0) min_dp = asm_opt.het_cov * RESEED_PEAK_RATE;
collect_no_cov_regions(olist, R_INF, b, r, min_dp, RESEED_LEN);
for (i = 0; i < (int)r->a.n; i++)
@@ -7291,21 +7296,86 @@ int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u32
if(fp) fprintf(fp, "qs: %d, qe: %d, ava_k_mer: %d, hp_k_mer: %d\n", qs, qe, ava_k_mer, hp_k_mer);
}
if(fp) fprintf(fp, "ava_k_mer: %d, hp_k_mer: %d, hp_rate: %f\n", ava_k_mer, hp_k_mer, hp_rate);
if(fp) fprintf(fp, "ava_k_mer: %d, hp_k_mer: %d, hp_rate: %f, min_dp: %d, a.n: %d\n", ava_k_mer, hp_k_mer, hp_rate, min_dp, (int)r->a.n);
if(fp)
{
for (k = 0; k < (int)k_flag->a.n; k++)
{
if(k_flag->a.a[k] > 0) fprintf(fp, "(%d) %u\n", k, k_flag->a.a[k]);
}
}
// if(fp)
// {
// for (k = 0; k < (int)k_flag->a.n; k++)
// {
// if(k_flag->a.a[k] > 0) fprintf(fp, "(%d) %u\n", k, k_flag->a.a[k]);
// }
// }
if(hp_k_mer > ava_k_mer*hp_rate) return 1; ///must use '>' instead of '>='
r->a.n = 0;
return 0;
}
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u8_warp* k_flag,
float hp_rate, int rlen, FILE* fp)
{
int i, ava_k_mer = 0, hp_k_mer = 0, vLen, min_dp;
int32_t w, n[4];
n[0] = n[1] = n[2] = n[3] = 0;
min_dp = RESEED_DP;
if(asm_opt.hom_cov > 0) min_dp = asm_opt.hom_cov * RESEED_PEAK_RATE;
if(min_dp > RESEED_DP) min_dp = RESEED_DP;
overlap_region* ov = NULL;
for (i = 0; i < (long long)olist->length; i++)
{
ov = &(olist->list[i]);
if (ov->is_match != 1 && ov->is_match != 2) continue;
w = ha_ov_type(ov, rlen);
++n[w];
}
if(fp) fprintf(fp, "n[0]: %d, n[1]: %d, n[2]: %d, n[3]: %d\n", n[0], n[1], n[2], n[3]);
// n[0] += n[2];
// n[1] += n[2];
if(n[0] < min_dp)
{
ava_k_mer = hp_k_mer = 0;
vLen = MIN(k_flag->a.n, RESEED_LEN);
for (i = 0; i < vLen; i++)
{
if(k_flag->a.a[i] > 1) ava_k_mer++;
if(k_flag->a.a[i] > 2) hp_k_mer++;
}
if(hp_k_mer > ava_k_mer*hp_rate) return 1;
}
if(n[1] < min_dp)
{
ava_k_mer = hp_k_mer = 0;
vLen = MIN(k_flag->a.n, RESEED_LEN);
for (i = k_flag->a.n - vLen; i < (int)k_flag->a.n; i++)
{
if(k_flag->a.a[i] > 1) ava_k_mer++;
if(k_flag->a.a[i] > 2) hp_k_mer++;
}
if(hp_k_mer > ava_k_mer*hp_rate) return 1;
}
if(fp) fprintf(fp, "ava_k_mer: %d, hp_k_mer: %d, hp_rate: %f, min_dp: %d\n", ava_k_mer, hp_k_mer, hp_rate, min_dp);
// if(fp)
// {
// for (k = 0; k < (int)k_flag->a.n; k++)
// {
// if(k_flag->a.a[k] > 0) fprintf(fp, "(%d) %u\n", k, k_flag->a.a[k]);
// }
// }
return 0;
}
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
Graph* g, Graph* DAGCon, Cigar_record* current_cigar,
Correct.h
+1 -1
View File
@@ -1173,7 +1173,7 @@ void correct_overlap_high_het(overlap_region_alloc* overlap_list, All_reads* R_I
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read);
long long get_affine_gap_score(overlap_region* ovc, UC_Read* g_read, UC_Read* overlap_read, uint8_t* x_num,
uint8_t* y_num, uint64_t EstimateXOlen, uint64_t EstimateYOlen);
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u32_warp* b, kvec_t_u64_warp* r, kvec_t_u8_warp* k_flag, float hp_rate, FILE* fp);
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u8_warp* k_flag, float hp_rate, int rlen, FILE* fp);
#define FORWARD_KSW 0
#define BACKWARD_KSW 1
Hash_Table.cpp
+124 -26
View File
@@ -305,6 +305,9 @@ void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
}
}
long long get_chainLen(long long x_beg, long long x_end, long long xLen,
long long y_beg, long long y_end, long long yLen)
{
@@ -337,6 +340,50 @@ long long get_chainLen(long long x_beg, long long x_end, long long xLen,
return x_end - x_beg + 1;
}
void debug_chain_single_site(k_mer_hit* a, long long a_n, Chain_Data* dp, int x_readLen, int y_readLen, int s_index)
{
long long j, current_j = s_index;
long long selfLen = 0, indels = 0;
long long distance_self_pos, distance_pos, distance_gap;
j = s_index;
while (j >= 0)
{
current_j = j;
j = dp->pre[j];
if(j != -1)
{
distance_self_pos = a[current_j].self_offset - a[j].self_offset;
distance_pos = a[current_j].offset - a[j].offset;
distance_gap = distance_pos > distance_self_pos? distance_pos - distance_self_pos : distance_self_pos - distance_pos;
indels += distance_gap;
selfLen += distance_self_pos;
}
fprintf(stderr, "j: %lld, score: %lld, occ: %d, pre_j: %lld\n",
current_j, (long long)dp->score[current_j], dp->occ[current_j], j);
}
fprintf(stderr, "s_self_offset: %u, s_offset: %u, e_self_offset: %u, e_offset: %u, ovlp length: %lld, x_readLen: %d, y_readLen: %d\n",
a[s_index].self_offset, a[s_index].offset, a[current_j].self_offset, a[current_j].offset,
get_chainLen(a[s_index].self_offset, a[current_j].self_offset, x_readLen,
a[s_index].offset, a[current_j].offset, y_readLen), x_readLen, y_readLen);
if(indels != dp->indels[s_index])
{
fprintf(stderr, "indels: %lld, dp->indels[i]: %ld\n", indels, (long)dp->indels[s_index]);
}
if(selfLen != dp->self_length[s_index])
{
fprintf(stderr, "selfLen: %lld, dp->self_length[i]: %ld\n", selfLen, (long)dp->self_length[s_index]);
}
fprintf(stderr,"\n");
}
int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc, double bw_thres)
{
int32_t i, tot_indel = 0, tot_len = 0;
@@ -348,7 +395,7 @@ int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc
if (i < n_a) return -1;
bw_pen = 1.0 / bw_thres;
dp->score[0] = a[0].good? min_sc : min_sc>>1;
dp->pre[0] = -1, dp->indels[0] = 0, dp->self_length[0] = 0;
dp->pre[0] = -1, dp->indels[0] = 0, dp->self_length[0] = 0, dp->occ[0] = 1;
for (i = 1; i < n_a; ++i) {
int32_t score, dg;
int32_t dx = (int32_t)a[i].offset - (int32_t)a[i-1].offset;
@@ -368,6 +415,7 @@ int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc
dp->pre[i] = i - 1;
dp->indels[i] = tot_indel;
dp->self_length[i] = tot_len;
dp->occ[i] = i + 1;
}
if (i < n_a) return -1;
return n_a;
@@ -391,16 +439,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
resize_Chain_Data(dp, a_n);
ret = ha_chain_check(a, a_n, dp, min_score, band_width_threshold);
/***************************************debug**************************************/
if(a_n > 0 && Get_NAME_LENGTH((R_INF),a[0].readID)==strlen("m64062_190803_042216/128778853/ccs"))
{
if (memcmp("m64062_190803_042216/128778853/ccs", Get_NAME((R_INF), a[0].readID),
Get_NAME_LENGTH((R_INF), a[0].readID)) == 0)
{
fprintf(stderr, "ret: %d\n", ret);
}
}
/***************************************debug**************************************/
if (ret > 0) {
a_n = ret;
goto skip_dp;
@@ -445,7 +484,8 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
///min distance
distance_min = distance_pos < distance_self_pos? distance_pos:distance_self_pos;
score = distance_min < min_score? distance_min : min_score;
if (!a[j].good) score >>= 1;
///if (!a[j].good) score = (score >> 1) + (score & 1);
if (!a[j].good) score >>= 1;
gap_rate = (double)((double)(total_indels)/(double)(total_self_length));
///if the gap rate > 0.06, score will be negative
@@ -454,7 +494,7 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
score += dp->score[j];
///find a new max score
if (score > max_score) {
if (score > max_score) {///must use > instead of >=
max_score = score;
max_j = j;
max_indels = total_indels;
@@ -476,10 +516,12 @@ void chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* resul
dp->pre[i] = max_j;
dp->indels[i] = max_indels;
dp->self_length[i] = max_self_length;
dp->occ[i] = 1;
if(max_j != -1) dp->occ[i] = dp->occ[max_j] + 1;
}
///debug_chain(a, a_n, dp);
skip_dp:
max_score = -1;
@@ -510,17 +552,6 @@ skip_dp:
}
/***************************************debug**************************************/
if(a_n > 0 && Get_NAME_LENGTH((R_INF),a[0].readID)==strlen("m64062_190803_042216/128778853/ccs"))
{
if (memcmp("m64062_190803_042216/128778853/ccs", Get_NAME((R_INF), a[0].readID),
Get_NAME_LENGTH((R_INF), a[0].readID)) == 0)
{
fprintf(stderr, "max_i: %lld\n", max_i);
}
}
/***************************************debug**************************************/
clear_fake_cigar(&(result->f_cigar));
///note a has been sorted by offset, that means has been sorted by query offset
i = max_i;
@@ -583,7 +614,7 @@ skip_dp:
}
}
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
void calculate_overlap_region_by_chaining_back(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end)
{
overlap_region tmp_region;
@@ -648,6 +679,71 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
destory_fake_cigar(&(tmp_region.f_cigar));
}
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end, overlap_region* f_cigar)
{
long long i = 0;
uint64_t current_ID;
uint64_t current_stand;
if (candidates->length == 0)
{
return;
}
long long sub_region_beg;
long long sub_region_end;
clear_fake_cigar(&((*f_cigar).f_cigar));
i = 0;
while (i < candidates->length)
{
chain_idx->a.n = 0;
current_ID = candidates->list[i].readID;
current_stand = candidates->list[i].strand;
///reference read
(*f_cigar).x_id = readID;
(*f_cigar).x_pos_strand = current_stand;
///query read
(*f_cigar).y_id = current_ID;
///here the strand of query is always 0
(*f_cigar).y_pos_strand = 0;
sub_region_beg = i;
sub_region_end = i;
i++;
while (i < candidates->length
&&
current_ID == candidates->list[i].readID
&&
current_stand == candidates->list[i].strand)
{
sub_region_end = i;
i++;
}
if ((*f_cigar).x_id == (*f_cigar).y_id)
{
continue;
}
chain_DP(candidates->list + sub_region_beg,
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), f_cigar, band_width_threshold,
25, Get_READ_LENGTH((*R_INF), (*f_cigar).x_id), Get_READ_LENGTH((*R_INF), (*f_cigar).y_id));
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if ((*f_cigar).x_id != (*f_cigar).y_id)
{
append_inexact_overlap_region_alloc(overlap_list, f_cigar, R_INF, add_beg_end);
}
}
}
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end, int error_threshold)
{
@@ -725,6 +821,7 @@ void destory_Chain_Data(Chain_Data* x)
free(x->pre);
free(x->indels);
free(x->self_length);
free(x->occ);
free(x->tmp);
}
@@ -737,6 +834,7 @@ void resize_Chain_Data(Chain_Data* x, long long size)
REALLOC(x->pre, x->size);
REALLOC(x->indels, x->size);
REALLOC(x->self_length, x->size);
REALLOC(x->occ, x->size);
REALLOC(x->tmp, x->size);
}
}
Hash_Table.h
+3 -2
View File
@@ -119,6 +119,7 @@ typedef struct {
int64_t *pre;
int32_t *indels;
int32_t *self_length;
int32_t *occ;
int64_t *tmp; // MUST BE 64-bit integer
int64_t length;
int64_t size;
@@ -144,8 +145,8 @@ int extra_begin, int extra_end, int error_threshold);
void overlap_region_sort_y_id(overlap_region *a, long long n);
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end);
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end, overlap_region* f_cigar);
void init_fake_cigar(Fake_Cigar* x);
void destory_fake_cigar(Fake_Cigar* x);
Process_Read.h
+2 -1
View File
@@ -22,7 +22,8 @@
///#define Get_READ(R_INF, ID) R_INF.read + (R_INF.index[ID]>>2) + ID
#define Get_READ(R_INF, ID) (R_INF).read_sperate[(ID)]
#define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
#define CHECK_BY_NAME(R_INF, NAME, ID) (Get_NAME_LENGTH((R_INF),(ID))==strlen((NAME)) && \
memcmp((NAME), Get_NAME((R_INF), (ID)), Get_NAME_LENGTH((R_INF),(ID))) == 0)
extern uint8_t seq_nt6_table[256];
extern char bit_t_seq_table[256][4];
anchor.cpp
+6 -18
View File
@@ -50,7 +50,7 @@ uint64_t ha_abuf_mem(const ha_abuf_t *ab)
return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(ha_mz1_t) + sizeof(seed1_t)) + sizeof(ha_abuf_t);
}
static int ha_ov_type(const overlap_region *r, uint32_t len)
int ha_ov_type(const overlap_region *r, uint32_t len)
{
if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 3; // containing a shorter read
@@ -58,7 +58,7 @@ static int ha_ov_type(const overlap_region *r, uint32_t len)
}
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag,
void *ha_flt_tab, ha_pt_t *ha_idx)
kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar)
{
uint32_t i, rlen;
uint64_t k, l;
@@ -130,22 +130,10 @@ void *ha_flt_tab, ha_pt_t *ha_idx)
p->offset = ab->a[k].other_off;
p->self_offset = ab->a[k].self_off;
p->good = ab->a[k].good;
/***************************************debug**************************************/
if(Get_NAME_LENGTH((R_INF),p->readID)==strlen("m64062_190803_042216/128778853/ccs"))
{
if (memcmp("m64062_190803_042216/128778853/ccs", Get_NAME((R_INF), p->readID),
Get_NAME_LENGTH((R_INF), p->readID)) == 0)
{
fprintf(stderr, "(%lu) readID: %u, strand: %u, offset: %u, self_offset: %u\n",
k, p->readID, p->strand, p->offset, p->self_offset);
}
}
/***************************************debug**************************************/
}
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain);
calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
#if 0
if (overlap_list->length > 0) {
@@ -217,14 +205,14 @@ void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf)
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
extern void *ha_flt_tab_hp;
extern ha_pt_t *ha_idx_hp;
ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, ha_flt_tab, ha_idx);
ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar);
if(ha_idx_hp)
{
@@ -254,7 +242,7 @@ int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, ma_hit_t_alloc* p
overlap_list->length = k;
ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, ha_flt_tab_hp, ha_idx_hp);
ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab_hp, ha_idx_hp, f_cigar);
if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
{