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fix bugs for overlaps of different length

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This commit is contained in:
Haoyu Cheng
2019-12-09 17:07:11 -05:00
parent fca9c8db15
commit 09603432e5
11 changed files with 1726 additions and 94 deletions
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Overlaps.h
+7 -1
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@@ -9,7 +9,8 @@
///#define MIN_OVERLAP_LEN 500
///#define MIN_OVERLAP_LEN 50
#define MIN_OVERLAP_LEN 50
#define MIN_OVERLAP_COVERAGE 1
///#define MIN_OVERLAP_COVERAGE 1
#define MIN_OVERLAP_COVERAGE 0
#define MAX_HANG_LEN 1000
#define MAX_HANG_PRE 0.8
#define GAP_FUZZ 1000
@@ -81,6 +82,7 @@ void debug_normalize_ma_hit_t(ma_hit_t_alloc* sources, long long num_sources);
typedef struct {
uint32_t s:31, del:1, e;
uint8_t c;
} ma_sub_t;
void ma_hit_sub(int min_dp, ma_hit_t_alloc* sources, long long n_read, uint64_t* readLen,
@@ -104,6 +106,7 @@ typedef struct {
typedef struct {
uint32_t len:31, del:1;
uint8_t c;
} asg_seq_t;
typedef struct {
@@ -324,4 +327,7 @@ 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 debug_info_of_specfic_read(char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, int id, char* command);
#endif