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change max coverage of pri-range

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chhylp123
2020-07-18 17:40:58 -04:00
parent 88ab801717
commit 952471657f
5 changed files with 76 additions and 51 deletions
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3
Assembly.cpp
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@@ -476,6 +476,7 @@ static void worker_ovec(void *data, long i, int tid)
int fully_cov, abnormal;
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1);
///ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.08, asm_opt.max_n_chain, 1);
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -514,6 +515,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
memcmp(asm_opt.required_read_name, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0)
{
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1);
///ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.08, asm_opt.max_n_chain, 1);
fprintf(stderr, ">%.*s\n", (int)Get_NAME_LENGTH((R_INF), i), Get_NAME((R_INF), i));
recover_UC_Read(&b->self_read, &R_INF, i);
@@ -957,6 +959,7 @@ static void worker_ov_final(void *data, long i, int tid)
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.001, asm_opt.max_n_chain, 0);
///ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.08, asm_opt.max_n_chain, 0);
/**
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,