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18 lines
997 B
C
18 lines
997 B
C
#ifndef __TOVLP__
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#define __TOVLP__
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#include <stdint.h>
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#include "Overlaps.h"
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utg_trans_t *init_utg_trans_t(ma_ug_t *ug, ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, R_to_U* ruIndex, asg_t *read_g, int max_hang, int min_ovlp);
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void destroy_utg_trans_t(utg_trans_t **o);
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void asg_bub_collect_ovlp(ma_ug_t *ug, uint32_t v0, buf_t *b, utg_trans_t *o);
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void collect_trans_ovlp(const char* cmd, buf_t* pri, uint64_t pri_offset, buf_t* aux, uint64_t aux_offset,
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ma_ug_t *ug, utg_trans_t *o);
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int asg_arc_decompress(asg_t *g, ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
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R_to_U* ruIndex, utg_trans_t *o);
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int asg_arc_decompress_mul(asg_t *g, ma_ug_t *ug, asg_t *read_sg, uint32_t positive_flag, uint32_t negative_flag,
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ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, utg_trans_t *o);
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kv_u_trans_t *pt_pdist(ma_ug_t *ug, asg_t *read_g, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources,
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kvec_asg_arc_t_warp* edge, int max_hang, int min_ovlp, uint32_t min_chain_cnt);
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#endif
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