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This commit is contained in:
Haoyu Cheng
2019-11-19 01:32:39 -05:00
parent ada03ea388
commit e8ff0c1dbc
2 changed files with 465 additions and 101 deletions
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Overlaps.cpp
+69 -24
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@@ -403,6 +403,8 @@ void normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources)
}
else
{
///must have this line
new_element.ml = 1;
set_reverse_overlap(&new_element, &(sources[i].buffer[j]));
add_ma_hit_t_alloc(&(sources[tn]), &new_element);
si_overlaps++;
@@ -5054,6 +5056,27 @@ long long weakID, uint32_t w_qs, uint32_t w_qe)
}
inline int check_weak_ma_hit_reverse(ma_hit_t_alloc* aim_paf, ma_hit_t_alloc* reverse_paf_list,
long long weakID)
{
long long i = 0;
long long strongID, index;
///all overlaps coming from another haplotye are strong
for (i = 0; i < aim_paf->length; i++)
{
strongID = Get_tn(aim_paf->buffer[i]);
index = get_specific_overlap
(&(reverse_paf_list[strongID]), strongID, weakID);
if(index != -1)
{
return 0;
}
}
return 1;
}
inline int check_weak_ma_hit_debug(ma_hit_t_alloc* aim_paf, ma_hit_t_alloc* reverse_paf_list,
long long weakID)
{
@@ -6897,6 +6920,17 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
uint32_t qn, tn;
ma_hit_t new_element;
long long qLen_0, qLen_1;
// if(memcmp("m64016_190918_162737/92668450/ccs", Get_NAME(R_INF, i),
// Get_NAME_LENGTH(R_INF, i)) == 0)
// {
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
// sources, reverse_sources, -1, "clean_weak_ma_hit_t");
// debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
// sources, reverse_sources, -1, "clean_weak_ma_hit_t");
// }
for (i = 0; i < num_sources; i++)
{
for (j = 0; j < sources[i].length; j++)
@@ -6907,20 +6941,13 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
//if this is a weak overlap
if(sources[i].buffer[j].ml == 0)
{
if(!check_weak_ma_hit(&(sources[qn]), reverse_sources, tn,
Get_qs(sources[i].buffer[j]), Get_qe(sources[i].buffer[j])))
if(
!check_weak_ma_hit(&(sources[qn]), reverse_sources, tn,
Get_qs(sources[i].buffer[j]), Get_qe(sources[i].buffer[j]))
/**
||
!check_weak_ma_hit_reverse(&(reverse_sources[qn]), sources, tn)**/)
{
/**
if(memcmp("m64016_190918_162737/76808505/ccs",
Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i)) == 0)
{
fprintf(stderr, "#### %.*s, %.*s\n",
Get_NAME_LENGTH(R_INF, qn), Get_NAME(R_INF, qn),
Get_NAME_LENGTH(R_INF, tn), Get_NAME(R_INF, tn));
}
**/
sources[i].buffer[j].bl = 0;
index = get_specific_overlap(&(sources[tn]), tn, qn);
sources[tn].buffer[index].bl = 0;
@@ -6929,6 +6956,8 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
}
}
long long m = 0;
long long pre_overlaps, current_overlaps, exact_overlaps;
exact_overlaps = pre_overlaps = current_overlaps = 0;
@@ -6954,10 +6983,17 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
current_overlaps += sources[i].length;
}
/**
fprintf(stdout, "pre_overlaps: %lld, current_overlaps: %lld, exact_overlaps: %lld\n",
pre_overlaps, current_overlaps, exact_overlaps);
**/
// if(memcmp("m64016_190918_162737/92668450/ccs", Get_NAME(R_INF, i),
// Get_NAME_LENGTH(R_INF, i)) == 0)
// {
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
// sources, reverse_sources, -1, "clean_weak_ma_hit_t");
// debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
// sources, reverse_sources, -1, "clean_weak_ma_hit_t");
// }
fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
}
@@ -7093,14 +7129,15 @@ ma_hit_t_alloc* reverse_sources, int id, char* command)
{
qn = Get_qn(sources[i].buffer[j]);
tn = Get_tn(sources[i].buffer[j]);
fprintf(stderr, "target: %.*s, qs: %d, qe: %d, ts: %d, te: %d, ml: %d, rev: %d\n",
fprintf(stderr, "target: %.*s, qs: %d, qe: %d, ts: %d, te: %d, ml: %d, rev: %d, el: %d\n",
Get_NAME_LENGTH(R_INF, tn), Get_NAME(R_INF, tn),
Get_qs(sources[i].buffer[j]),
Get_qe(sources[i].buffer[j]),
Get_ts(sources[i].buffer[j]),
Get_te(sources[i].buffer[j]),
sources[i].buffer[j].ml,
sources[i].buffer[j].rev);
sources[i].buffer[j].rev,
sources[i].buffer[j].el);
@@ -7419,16 +7456,24 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
}
// debug_info_of_specfic_read("m64016_190918_162737/72220752/ccs",
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
// sources, reverse_sources, -1, "init");
debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
sources, reverse_sources, -1, "init");
ma_sub_t* coverage_cut;
normalize_ma_hit_t(sources, n_read);
///normalize_ma_hit_t_single_side(sources, n_read);
///normalize_ma_hit_t(sources, n_read);
normalize_ma_hit_t_single_side(sources, n_read);
// debug_info_of_specfic_read("m64016_190918_162737/72220752/ccs",
// debug_info_of_specfic_read("m64016_190918_162737/92668450/ccs",
// sources, reverse_sources, -1, "normalize");
debug_info_of_specfic_read("m64016_190918_162737/53545052/ccs",
sources, reverse_sources, -1, "normalize");
@@ -7444,7 +7489,7 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
// debug_info_of_specfic_read("m64016_190918_162737/72220752/ccs",
// debug_info_of_specfic_read("m64016_190918_162737/49678749/ccs",
// sources, reverse_sources, -1, "clean");