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Merge branch 'master' into dev-lh3

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This commit is contained in:
Heng Li
2021-03-02 19:27:44 -05:00
parent 205eadf346 d2ca12604b
commit 8e98fb2276
17 changed files with 16486 additions and 4393 deletions
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CommandLines.h
+21 -1
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@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.13-r334-dirty"
#define HA_VERSION "0.14-r312"
#define VERBOSE 0
@@ -21,6 +21,11 @@
#define HA_MIN_OV_DIFF 0.02 // min sequence divergence in an overlap
typedef struct{
int *l, n;
char **a;
}enzyme;
typedef struct {
int flag;
int num_reads;
@@ -30,9 +35,13 @@ typedef struct {
char *fn_bin_yak[2];
char *fn_bin_list[2];
char *extract_list;
enzyme *hic_reads[2];
enzyme *hic_enzymes;
int extract_iter;
int thread_num;
int k_mer_length;
int hic_mer_length;
int bub_mer_length;
int mz_win;
int mz_sample_dist;
int bf_shift;
@@ -42,6 +51,9 @@ typedef struct {
double max_ov_diff_final;
int hom_cov;
int het_cov;
int b_low_cov;
int b_high_cov;
double m_rate;
int max_n_chain; // fall-back max number of chains to consider
int min_hist_kmer_cnt;
int load_index_from_disk;
@@ -60,15 +72,18 @@ typedef struct {
int purge_level_primary;
int purge_level_trio;
int purge_overlap_len;
int purge_overlap_len_hic;
int recover_atg_cov_min;
int recover_atg_cov_max;
int hom_global_coverage;
int bed_inconsist_rate;
int hic_inconsist_rate;
float max_hang_rate;
float min_drop_rate;
float max_drop_rate;
float purge_simi_rate;
float purge_simi_rate_hic;
long long small_pop_bubble_size;
long long large_pop_bubble_size;
@@ -94,4 +109,9 @@ static inline int ha_opt_triobin(const hifiasm_opt_t *opt)
return ((opt->fn_bin_yak[0] && opt->fn_bin_yak[1]) || (opt->fn_bin_list[0] && opt->fn_bin_list[1]));
}
static inline int ha_opt_hic(const hifiasm_opt_t *opt)
{
return ((opt->hic_reads[0] && opt->hic_reads[1]));
}
#endif