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update k-mer peaks

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chhylp123
2020-07-07 13:20:25 -04:00
parent 2e56ef7db5
commit a25c37ed89
9 changed files with 106 additions and 28 deletions
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Purge_Dups.cpp
+23 -22
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@@ -173,7 +173,7 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
}
}
print_peak(cov_buf, cov_buf_length, max_i);
///print_peak(cov_buf, cov_buf_length, max_i);
// look for smaller peak on the low end
max2 = -1; max2_i = -1;
@@ -190,7 +190,7 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
}
}
fprintf(stderr, "***max2: %lld, max2_i: %lld\n", max2, max2_i);
///fprintf(stderr, "***max2: %lld, max2_i: %lld\n", max2, max2_i);
if (max2_i != -1 && max2_i > err_i && max2_i < max_i)
{
@@ -219,7 +219,7 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
}
}
fprintf(stderr, "***max3: %lld, max3_i: %lld\n", max3, max3_i);
///fprintf(stderr, "***max3: %lld, max3_i: %lld\n", max3, max3_i);
//if found a peak
if (max3 != -1 && max3_i > max_i)
@@ -245,7 +245,7 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
(*het_peak) = max_i;
}
fprintf(stderr, "topo_peak: %lld, topo_peak_i: %lld\n", topo_peak, topo_peak_i);
///fprintf(stderr, "topo_peak: %lld, topo_peak_i: %lld\n", topo_peak, topo_peak_i);
}
@@ -262,10 +262,14 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
(*hom_peak) = max_i;
}
fprintf(stderr, "max: %lld, max_i: %lld\n", max, max_i);
fprintf(stderr, "max2: %lld, max2_i: %lld\n", max2, max2_i);
fprintf(stderr, "max3: %lld, max3_i: %lld\n", max3, max3_i);
fprintf(stderr, "(*het_peak): %lld, (*hom_peak): %lld\n", (*het_peak), (*hom_peak));
// fprintf(stderr, "max: %lld, max_i: %lld\n", max, max_i);
// fprintf(stderr, "max2: %lld, max2_i: %lld\n", max2, max2_i);
// fprintf(stderr, "max3: %lld, max3_i: %lld\n", max3, max3_i);
fprintf(stderr, "[M::%s] Heterozygous k-mer peak: %d\n", __func__, asm_opt.het_cov);
fprintf(stderr, "[M::%s] Homozygous k-mer peak: %d\n", __func__, asm_opt.hom_cov);
fprintf(stderr, "[M::%s] Heterozygous coverage peak: %lld\n", __func__, (*het_peak));
fprintf(stderr, "[M::%s] Homozygous coverage peak: %lld\n", __func__, (*hom_peak));
fprintf(stderr, "[M::%s] Alter coverage peak: %lld\n", __func__, topo_peak_i);
}
@@ -274,9 +278,12 @@ void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo
long long get_alter_peak(ma_ug_t *ug, asg_t *read_g, R_to_U* ruIndex, uint64_t* position_index,
ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
{
#define ALTER_COV_THRES 0.9
#define REAL_ALTER_THRES 0.1
ma_utg_t* u = NULL;
asg_t* nsg = ug->g;
uint64_t v, j, k, qn, n_vtx = nsg->n_seq;
uint64_t v, j, k, qn, n_vtx = nsg->n_seq, primary_bases = 0, alter_bases = 0;
uint32_t tn, is_Unitig;
long long* cov_buf = NULL;
ma_hit_t *h;
@@ -295,6 +302,8 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
{
qn = u->a[k]>>33;
position_index[qn] = 0;
R_bases = coverage_cut[qn].e - coverage_cut[qn].s;
primary_bases += R_bases;
}
}
@@ -305,6 +314,7 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
C_bases = C_bases_primary = C_bases_alter = 0;
R_bases = coverage_cut[qn].e - coverage_cut[qn].s;
alter_bases += R_bases;
for (j = 0; j < (uint64_t)(sources[qn].length); j++)
{
h = &(sources[qn].buffer[j]);
@@ -335,16 +345,7 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
// }
C_bases = C_bases_primary + C_bases_alter;
if(C_bases_alter < C_bases * 0.8) continue;
///fprintf(stderr, "******************qn: %lu\n",qn);
/**
if(qn == 1893151 || qn == 1929038)
{
fprintf(stderr, "******************qn: %lu\n",
qn);
}
**/
if(C_bases_alter < C_bases * ALTER_COV_THRES) continue;
C_bases = C_bases/R_bases;
if(C_bases < 0 || C_bases >= cov_buf_length) continue;
@@ -361,9 +362,9 @@ ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
}
}
fprintf(stderr, "alter max_i: %lld, max: %lld\n", max_i, max);
if(max_i < 5) max_i = max = -1;
///fprintf(stderr, "alter max_i: %lld, max: %lld\n", max_i, max);
///if(max_i < 5) max_i = max = -1;
if(alter_bases < primary_bases * REAL_ALTER_THRES) max_i = max = -1;
free(cov_buf);
memset(position_index, -1, sizeof(uint64_t)*read_g->n_seq);