xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-04 04:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

small bugs fixed

Browse Source
This commit is contained in:
chhylp123
2022-05-14 22:07:55 -04:00
parent 832e43fe3b
commit 74ad15846e
4 changed files with 281 additions and 147 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+39 -23
View File
@@ -24825,12 +24825,16 @@ char* output_file_name, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, all_ul
write_debug_ma_hit_ts(sources, R_INF.total_reads, gfa_name);
sprintf(gfa_name, "%s.all.debug.reverse", output_file_name);
write_debug_ma_hit_ts(reverse_sources, R_INF.total_reads, gfa_name);
sprintf(gfa_name, "%s.all.debug.coverage_cut", output_file_name);
write_coverage_cut(coverage_cut, gfa_name, R_INF.total_reads);
if(coverage_cut) {
sprintf(gfa_name, "%s.all.debug.coverage_cut", output_file_name);
write_coverage_cut(coverage_cut, gfa_name, R_INF.total_reads);
}
sprintf(gfa_name, "%s.all.debug.ruIndex", output_file_name);
write_ruIndex(ruIndex, gfa_name);
sprintf(gfa_name, "%s.all.debug.asg_t", output_file_name);
write_asg_t(sg, gfa_name);
if(sg) {
sprintf(gfa_name, "%s.all.debug.asg_t", output_file_name);
write_asg_t(sg, gfa_name);
}
if(ul_r_inf) {
sprintf(gfa_name, "%s.all.debug.ul.rinfor", output_file_name);
write_all_ul_t(ul_r_inf, gfa_name, NULL);
@@ -24850,19 +24854,22 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex, all_u
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
sprintf(gfa_name, "%s.all.debug.reverse.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
sprintf(gfa_name, "%s.all.debug.coverage_cut.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
if(coverage_cut) {
sprintf(gfa_name, "%s.all.debug.coverage_cut.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
}
sprintf(gfa_name, "%s.all.debug.ruIndex.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
sprintf(gfa_name, "%s.all.debug.asg_t.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
if(sg) {
sprintf(gfa_name, "%s.all.debug.asg_t.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
}
if(ul_r_inf) {
sprintf(gfa_name, "%s.all.debug.ul.rinfor.ul.ovlp.bin", output_file_name);
fp = fopen(gfa_name, "r"); if(!fp) return 0; fclose(fp);
}
if((sg == NULL) || (sources == NULL) || (coverage_cut == NULL) || (reverse_sources == NULL) ||
(ruIndex == NULL))
if((sources == NULL) || (reverse_sources == NULL) || (ruIndex == NULL))
{
return 1;
}
@@ -24877,7 +24884,7 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex, all_u
destory_ma_hit_t_alloc((*reverse_sources));
}
if((*coverage_cut)!=NULL)
if(coverage_cut && (*coverage_cut)!=NULL)
{
free((*coverage_cut));
}
@@ -24887,7 +24894,7 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex, all_u
destory_R_to_U((ruIndex));
}
if((*sg)!=NULL)
if(sg && (*sg)!=NULL)
{
asg_destroy(*sg);
}
@@ -24906,10 +24913,12 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex, all_u
return 0;
}
sprintf(gfa_name, "%s.all.debug.coverage_cut", output_file_name);
if(!load_coverage_cut(coverage_cut, gfa_name))
{
return 0;
if(coverage_cut) {
sprintf(gfa_name, "%s.all.debug.coverage_cut", output_file_name);
if(!load_coverage_cut(coverage_cut, gfa_name))
{
return 0;
}
}
sprintf(gfa_name, "%s.all.debug.ruIndex", output_file_name);
@@ -24918,11 +24927,14 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex, all_u
return 0;
}
sprintf(gfa_name, "%s.all.debug.asg_t", output_file_name);
if(!load_asg_t(sg, gfa_name))
{
return 0;
if(sg) {
sprintf(gfa_name, "%s.all.debug.asg_t", output_file_name);
if(!load_asg_t(sg, gfa_name))
{
return 0;
}
}
if(ul_r_inf) {
sprintf(gfa_name, "%s.all.debug.ul.rinfor", output_file_name);
@@ -31446,7 +31458,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
if(debug_g)
{
init_bub_label_t(&b_mask_t, MIN(10, asm_opt.thread_num), sg->n_seq);
init_bub_label_t(&b_mask_t, MIN(10, asm_opt.thread_num), n_read);
goto debug_gfa;
}
///just for debug
@@ -31468,6 +31480,11 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t));
}
// if (asm_opt.flag & HA_F_VERBOSE_GFA) {
// write_debug_graph(NULL, sources, coverage_cut, output_file_name, reverse_sources, ruIndex, &UL_INF);
// debug_gfa:;
// }
///should recover edges from sources by using UL alignments
if(asm_opt.ar) create_ul_info(sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex);
@@ -31510,7 +31527,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
write_debug_graph(sg, sources, coverage_cut, output_file_name, reverse_sources, ruIndex, &UL_INF);
debug_gfa:;
gen_ug_opt_t(&uopt, sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex);
// if(asm_opt.ar) create_ul_info(sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz, min_dp, readLen, coverage_cut, ruIndex);
}
if(asm_opt.ar) ul_realignment_gfa(&uopt, sg);
print_debug_gfa(sg, NULL, coverage_cut, "UL.debug", sources, ruIndex, max_hang_length, mini_overlap_length);
@@ -31722,7 +31738,7 @@ long long bubble_dist, int read_graph, int write)
min_thres = asm_opt.max_short_tip + 1;
if (asm_opt.flag & HA_F_VERBOSE_GFA)
{
if(load_debug_graph(&sg, &sources, &coverage_cut, output_file_name, &reverse_sources, &ruIndex, &UL_INF))
if(load_debug_graph(/**NULL**/&sg, &sources, /**NULL**/&coverage_cut, output_file_name, &reverse_sources, &ruIndex, &UL_INF))
{
fprintf(stderr, "debug gfa has been loaded\n");