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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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94
Correct.cpp
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@@ -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,