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ont overlapping

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chhylp123
2024-12-21 03:17:17 -05:00
parent 3067771783
commit 2c77b3c87e
6 changed files with 170 additions and 4 deletions
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30
Assembly.cpp
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@@ -1050,6 +1050,21 @@ void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t
}
int ha_ec_dbg(void)
{
int hom_cov, het_cov;
ha_idx = ha_pt_gen(&asm_opt, 0, 0, 0, &R_INF, &hom_cov, &het_cov); // build the index
asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
ha_opt_update_cov(&asm_opt, hom_cov);
cal_ec_r_dbg(asm_opt.thread_num, R_INF.total_reads);
ha_pt_destroy(ha_idx); ha_idx = NULL;
return 0;
}
void ha_overlap_and_correct(int round)
{
int i, hom_cov, het_cov, r_out = 0;
@@ -2003,8 +2018,7 @@ int ha_assemble_ovec(void)
ha_flt_tab = ha_idx = NULL;
// construct hash table for high occurrence k-mers
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL)
{
if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
ha_opt_update_cov(&asm_opt, hom_cov);
}
@@ -2026,6 +2040,18 @@ int ha_assemble_ovec(void)
return 0;
}
int ha_assemble_ovec_cc(void)
{
ha_idx = NULL;
ha_opt_reset_to_round(&asm_opt, 0); // this update asm_opt.roundID and a few other fields
ha_ec_dbg();
// Output_PAF0(R_INF.paf, "0");
destory_All_reads(&R_INF);
return 0;
}
int ha_assemble(void)
{
// debug_mc_g_t(MC_NAME);