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update trans chain

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chhylp123
2021-03-10 22:46:50 -05:00
parent 8aa87fdce8
commit 4c2ce6fc6b
6 changed files with 1363 additions and 334 deletions
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Purge_Dups.h
+3 -3
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@@ -16,13 +16,13 @@
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
uint32_t purege_minLen, int max_hang, int min_ovlp, long long bubble_dist, float drop_ratio,
uint32_t just_contain, uint32_t just_coverage, hc_links* link, hap_cov_t *cov);
uint32_t just_contain, uint32_t just_coverage, hap_cov_t *cov);
void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge,
uint32_t is_circle, uint64_t* rLen);
void get_contig_length(ma_ug_t *ug, asg_t *g, uint64_t* primaryLen, uint64_t* alterLen);
void enable_debug_mode(uint32_t mode);
hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex,
ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, int max_hang, int min_ovlp);
hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources,
ma_sub_t *coverage_cut, int max_hang, int min_ovlp, hc_links* link);
void destory_hap_cov_t(hap_cov_t **x);
void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);