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24 lines
1.9 KiB
C
24 lines
1.9 KiB
C
#ifndef __GFA_UT__
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#define __GFA_UT__
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#include "Overlaps.h"
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void ul_clean_gfa(ug_opt_t *uopt, asg_t *sg, ma_hit_t_alloc *src, ma_hit_t_alloc *rev, R_to_U* rI, int64_t clean_round, double min_ovlp_drop_ratio, double max_ovlp_drop_ratio,
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double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, int32_t is_ou, int32_t is_trio, uint32_t ou_thres, char *o_file);
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uint32_t asg_arc_cut_tips(asg_t *g, uint32_t max_ext, asg64_v *in, uint32_t is_ou, R_to_U *ru);
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void asg_iterative_semi_circ(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_t normal_len, uint32_t pop_chimer, asg64_v *dbg);
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void asg_arc_cut_chimeric(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, uint32_t ou_thres);
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void asg_arc_cut_inexact(asg_t *g, ma_hit_t_alloc* src, asg64_v *in, int32_t max_ext, uint32_t is_ou, uint32_t is_trio, float ou_rat/**, asg64_v *dbg**/);
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void asg_arc_cut_length(asg_t *g, asg64_v *in, int32_t max_ext, float len_rat, float ou_rat, uint32_t is_ou, uint32_t is_trio,
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uint32_t is_topo, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len);
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void asg_arc_cut_bub_links(asg_t *g, asg64_v *in, float len_rat, float sec_len_rat, float ou_rat, uint32_t is_ou, uint64_t check_dist, ma_hit_t_alloc *rev, R_to_U* rI, int32_t max_ext);
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void asg_arc_cut_complex_bub_links(asg_t *g, asg64_v *in, float len_rat, float ou_rat, uint32_t is_ou, bub_label_t *b_mask_t);
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uint32_t asg_cut_large_indel(asg_t *g, asg64_v *in, int32_t max_ext, float ou_rat, uint32_t is_ou);
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uint32_t asg_cut_semi_circ(asg_t *g, uint32_t lim_len, uint32_t is_clean);
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void ul_realignment_gfa(ug_opt_t *uopt, asg_t *sg, int64_t clean_round, double min_ovlp_drop_ratio,
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double max_ovlp_drop_ratio, int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio);
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void recover_contain_g(asg_t *g, ma_hit_t_alloc *src, R_to_U* ruIndex, int64_t max_hang, int64_t min_ovlp, int64_t ul_occ);
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void normalize_gou(asg_t *g);
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void prt_specfic_sge(asg_t *g, uint32_t src, uint32_t dst, const char* cmd);
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#endif
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