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haplotype popping

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chhylp123
2021-05-24 19:43:50 -04:00
parent 9e6dde7fb2
commit a39f01f4d8
9 changed files with 1696 additions and 567 deletions
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Purge_Dups.h
+1 -1
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@@ -75,7 +75,7 @@ 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, uint32_t is_collect_trans);
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);
void chain_trans_ovlp(hap_cov_t *cov, utg_trans_t *o, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t* types);
void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp);