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24 lines
910 B
C
24 lines
910 B
C
#ifndef __PURGEDUPS__
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#define __PURGEDUPS__
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#include <stdio.h>
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#include <stdint.h>
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#include "kvec.h"
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#include "kdq.h"
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#include "Overlaps.h"
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#include "Hash_Table.h"
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#define COV_COUNT 1024
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#define HOM_PEAK_RATE 1.25
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#define HET_PEAK_RATE (HOM_PEAK_RATE*2)
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#define ALTER_COV_THRES 0.9
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#define REAL_ALTER_THRES 0.1
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void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
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ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density,
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uint32_t purege_minLen, int max_hang, int min_ovlp, long long bubble_dist, float drop_ratio,
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uint32_t just_contain, uint32_t just_coverage);
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void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge,
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uint32_t is_circle, uint64_t* rLen);
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void get_contig_length(ma_ug_t *ug, asg_t *g, uint64_t* primaryLen, uint64_t* alterLen);
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void enable_debug_mode(uint32_t mode);
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#endif |