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r502->additional alignment

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chhylp123
2023-01-25 09:39:41 -05:00
parent 78ef43ce8e
commit 1166b92eb4
8 changed files with 228 additions and 70 deletions
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inter.cpp
+9 -5
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@@ -16125,13 +16125,13 @@ void trans_base_infer(ma_ug_t *ug, asg_t *sg, ug_opt_t *uopt, kv_u_trans_t *res,
}
ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg, uint32_t double_check_cache)
ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg, uint32_t double_check_cache, const char *bin_file)
{
fprintf(stderr, "[M::%s::] ==> starting UL\n", __func__);
mg_idxopt_t opt; uldat_t sl;
int32_t cutoff;
char* gfa_name = NULL; MALLOC(gfa_name, strlen(asm_opt.output_file_name)+50);
sprintf(gfa_name, "%s.%s", asm_opt.output_file_name, HA_RE_UL_ID);
sprintf(gfa_name, "%s.%s", asm_opt.output_file_name, bin_file);
init_aux_table(); ha_opt_update_cov(&asm_opt, asm_opt.hom_cov);
cutoff = REA_ALIGN_CUTOFF;
@@ -16147,9 +16147,13 @@ ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg, uint32_t double_check_c
gen_UL_reovlps(&sl, ug, sg, gfa_name, cutoff);
// exit(1);
write_all_ul_t(&UL_INF, gfa_name, ug);
} else if(double_check_cache){
if(drenew_UL_reovlps(&sl, ug, sg, gfa_name, cutoff)) {
write_all_ul_t(&UL_INF, gfa_name, ug);
} else{
free(UL_INF.ridx.idx.a); free(UL_INF.ridx.occ.a);
memset(&(UL_INF.ridx), 0, sizeof((UL_INF.ridx)));
if(double_check_cache){
if(drenew_UL_reovlps(&sl, ug, sg, gfa_name, cutoff)) {
write_all_ul_t(&UL_INF, gfa_name, ug);
}
}
}