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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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Overlaps.h
+11 -34
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@@ -3,7 +3,6 @@
#include <stdint.h>
#include "kvec.h"
#include "kdq.h"
///#include "Hash_Table.h"
///#define MIN_OVERLAP_LEN 2000
///#define MIN_OVERLAP_LEN 500
@@ -68,16 +67,7 @@ void ma_hit_sort_qns(ma_hit_t *a, long long n);
int load_all_data_from_disk(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources,
char* output_file_name);
typedef struct {
ma_hit_t_alloc overlaps;
} Assembly_Graph;
void init_Assembly_Graph(Assembly_Graph* x);
void destory_Assembly_Graph(Assembly_Graph* x);
void collect_ma_hit_t(ma_hit_t_alloc* dest, ma_hit_t_alloc* sources, long long num_sources);
void normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources);
void debug_normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources);
typedef struct {
@@ -93,7 +83,6 @@ void ma_hit_flt(ma_hit_t_alloc* sources, long long n_read, const ma_sub_t *cover
int max_hang, int min_ovlp);
long long get_specific_overlap(ma_hit_t_alloc* x, uint32_t qn, uint32_t tn);
void debug_cut_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources, ma_sub_t *coverage_cut);
typedef struct {
uint64_t ul;
@@ -139,7 +128,7 @@ static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, fl
///ext5 and ext3 is the hang on left side and right side, respectively
ext5 = qs < tl5? qs : tl5;
ext3 = ql - h->qe < tl3? ql - h->qe : tl3;
ext3 = ql - (int)h->qe < tl3? ql - (int)h->qe : tl3;
/**
@@ -179,11 +168,11 @@ static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, fl
********************************target-to-query overlap****************************
**/
if (qs <= tl5 && ql - h->qe <= tl3) return MA_HT_QCONT; // query contained in target
else if (qs >= tl5 && ql - h->qe >= tl3) return MA_HT_TCONT; // target contained in query
if (qs <= tl5 && ql - (int)h->qe <= tl3) return MA_HT_QCONT; // query contained in target
else if (qs >= tl5 && ql - (int)h->qe >= tl3) return MA_HT_TCONT; // target contained in query
else if (qs > tl5) u = 0, v = !!h->rev, l = qs - tl5; ///u = 0 means query-to-target overlap, l is the length of node in string graph (not the overlap length)
else u = 1, v = !h->rev, l = (ql - h->qe) - tl3; ///u = 1 means target-to-query overlaps, l is the length of node in string graph (not the overlap length)
if (h->qe - qs + ext5 + ext3 < min_ovlp || h->te - h->ts + ext5 + ext3 < min_ovlp) return MA_HT_SHORT_OVLP; // short overlap
if ((int)h->qe - qs + ext5 + ext3 < min_ovlp || (int)h->te - (int)h->ts + ext5 + ext3 < min_ovlp) return MA_HT_SHORT_OVLP; // short overlap
///u = 0 / 1 means query-to-target / target-to-query overlaps,
///l is the length of node in string graph (not the overlap length between two reads)
u |= h->qns>>32<<1, v |= h->tn<<1;
@@ -206,11 +195,6 @@ static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, fl
}
void build_string_graph(int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long n_read, uint64_t* readLen,
long long mini_overlap_length, long long max_hang_length,
long long clean_round, float min_ovlp_drop_ratio, float max_ovlp_drop_ratio,
float final_ovlp_drop_ratio, char* output_file_name, long long bubble_dist);
#define asg_arc_len(arc) ((uint32_t)(arc).ul)
#define asg_arc_n(g, v) ((uint32_t)(g)->idx[(v)])
@@ -296,13 +280,7 @@ typedef struct {
// count the number of outgoing arcs, including reduced arcs
static inline int count_out_with_del(const asg_t *g, uint32_t v)
{
uint32_t i, n, nv = asg_arc_n(g, v);
const asg_arc_t *av = asg_arc_a(g, v);
/**
for (i = n = 0; i < nv; ++i)
if (!av[i].del) ++n;
return n;
**/
uint32_t nv = asg_arc_n(g, v);
return nv;
}
@@ -318,14 +296,13 @@ static inline int count_out_without_del(const asg_t *g, uint32_t v)
return n;
}
void debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, int id, char* fun);
void build_string_graph_without_clean(int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long n_read, uint64_t* readLen,
long long mini_overlap_length, long long max_hang_length,
long long clean_round, float min_ovlp_drop_ratio, float max_ovlp_drop_ratio,
float corase_ovlp_drop_ratio, char* output_file_name, long long bubble_dist, int read_graph,
int write);
void build_string_graph_without_clean(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
long long max_hang_length, long long clean_round, long long pop_bubble_size,
float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, int write);
void debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, int id, char* command);