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same haplotype chimeric reads detection

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Haoyu Cheng
2019-12-24 14:43:12 -05:00
parent 29fe35eb21
commit 7f9c73507d
1 changed files with 10 additions and 10 deletions
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Overlaps.cpp
+10 -10
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@@ -1415,7 +1415,7 @@ void print_overlaps(ma_hit_t_alloc* paf, long long rLen, long long interval_s, l
} }
void detect_chimeric_reads(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, void detect_chimeric_reads(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf_x,
long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate) long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
{ {
double startTime = Get_T(); double startTime = Get_T();
@@ -1435,7 +1435,7 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
max_left.s = max_right.s = rLen; max_left.s = max_right.s = rLen;
max_left.e = max_right.e = 0; max_left.e = max_right.e = 0;
// if(i == 5783410) // if(i == 6937245)
// { // {
// fprintf(stderr, "\n\npaf: \n"); // fprintf(stderr, "\n\npaf: \n");
// print_overlaps(&paf[i], rLen, interval_s, interval_e); // print_overlaps(&paf[i], rLen, interval_s, interval_e);
@@ -1445,7 +1445,7 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
collect_sides(&(paf[i]), rLen, &max_left, &max_right); collect_sides(&(paf[i]), rLen, &max_left, &max_right);
collect_sides(&(rev_paf[i]), rLen, &max_left, &max_right); ///collect_sides(&(rev_paf[i]), rLen, &max_left, &max_right);
///that means this read is an end node ///that means this read is an end node
if(max_left.s == rLen || max_right.s == rLen) if(max_left.s == rLen || max_right.s == rLen)
{ {
@@ -1453,17 +1453,17 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
} }
// if(i == 5783410) // if(i == 6937245)
// { // {
// fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n", // fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n",
// max_left.s, max_left.e, max_right.s, max_right.e); // max_left.s, max_left.e, max_right.s, max_right.e);
// } // }
collect_contain(&(paf[i]), &(rev_paf[i]), rLen, &max_left, &max_right, 0.1); collect_contain(&(paf[i]), NULL, rLen, &max_left, &max_right, 0.1);
///collect_contain(&(rev_paf[i]), rLen, &max_left, &max_right); ///collect_contain(&(paf[i]), &(rev_paf[i]), rLen, &max_left, &max_right, 0.1);
// if(i == 5783410) // if(i == 6937245)
// { // {
// fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n", // fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n",
// max_left.s, max_left.e, max_right.s, max_right.e); // max_left.s, max_left.e, max_right.s, max_right.e);
@@ -1490,7 +1490,7 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
continue; continue;
} }
// if(i == 5783410) // if(i == 6937245)
// { // {
// fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n", // fprintf(stderr, "max_left.s: %d, max_left.e: %d, max_right.s: %d, max_right.e: %d\n",
// max_left.s, max_left.e, max_right.s, max_right.e); // max_left.s, max_left.e, max_right.s, max_right.e);
@@ -1517,8 +1517,8 @@ long long n_read, uint64_t* readLen, ma_sub_t* coverage_cut, float shift_rate)
kv_resize(char, b_q, WINDOW*4+20); kv_resize(char, b_q, WINDOW*4+20);
kv_resize(char, b_t, WINDOW*4+20); kv_resize(char, b_t, WINDOW*4+20);
if(intersection_check_by_base(&(paf[i]), rLen, interval_s, interval_e, b_q.a, b_t.a) if(intersection_check_by_base(&(paf[i]), rLen, interval_s, interval_e, b_q.a, b_t.a)
|| /**||
intersection_check_by_base(&(rev_paf[i]), rLen, interval_s, interval_e, b_q.a, b_t.a)) intersection_check_by_base(&(rev_paf[i]), rLen, interval_s, interval_e, b_q.a, b_t.a)**/)
{ {
coverage_cut[i].c = 1; coverage_cut[i].c = 1;
coverage_cut[i].del = 1; coverage_cut[i].del = 1;