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bug fix for bubble scanning

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chhylp123
2021-04-23 20:40:43 -04:00
parent a5b29b00bd
commit 7b07e355b7
8 changed files with 183 additions and 97 deletions
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Assembly.cpp
+2
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@@ -10,6 +10,7 @@
#include "Correct.h"
#include "htab.h"
#include "kthread.h"
#include "rcut.h"
void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct);
@@ -1605,6 +1606,7 @@ void ha_overlap_final(void)
int ha_assemble(void)
{
// debug_mc_g_t(MC_NAME);
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r, hom_cov = -1, ovlp_loaded = 0;
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {