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r189: print statistics

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This commit is contained in:
Heng Li
2020-04-04 00:14:53 -04:00
parent 69c32066d4
commit dbe66d259d
3 changed files with 25 additions and 55 deletions
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Assembly.cpp
+24 -51
View File
@@ -475,16 +475,7 @@ void* Overlap_calculate_heap_merge(void* arg)
asm_opt.num_bases += num_read_base;
asm_opt.num_corrected_bases += num_correct_base;
asm_opt.num_recorrected_bases += num_recorrect_base;
asm_opt.complete_threads++;
if(asm_opt.complete_threads == asm_opt.thread_num)
{
fprintf(stderr, "total bases #: %lld\n", asm_opt.num_bases);
fprintf(stderr, "total corrected bases: %lld\n", asm_opt.num_corrected_bases);
fprintf(stderr, "total recorrected bases: %lld\n", asm_opt.num_recorrected_bases);
}
pthread_mutex_unlock(&statistics);
return NULL;
}
@@ -799,40 +790,31 @@ void update_exact_overlaps(overlap_region_alloc* overlap_list, UC_Read* g_read,
}
}
void statistic(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, long long readNum)
void ha_print_ovlp_stat(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, long long readNum)
{
long long forward, reverse, strong, weak, exact, no_l_indel;
long long i, j;
long long forward, reverse, strong, weak, exact, no_l_indel;
no_l_indel = forward = reverse = exact = strong = weak = 0;
long long i, j;
for (i = 0; i < readNum; i++)
{
forward += paf[i].length;
reverse += rev_paf[i].length;
for (j = 0; j < paf[i].length; j++)
{
if(paf[i].buffer[j].el == 1) exact++;
if(paf[i].buffer[j].ml == 1) strong++;
if(paf[i].buffer[j].ml == 0) weak++;
if(paf[i].buffer[j].no_l_indel == 1) no_l_indel++;
}
}
fprintf(stderr, "****************statistic for overlaps****************\n");
fprintf(stderr, "overlaps #: %lld\n", forward);
fprintf(stderr, "strong overlaps #: %lld\n", strong);
fprintf(stderr, "weak overlaps #: %lld\n", weak);
fprintf(stderr, "exact overlaps #: %lld\n", exact);
fprintf(stderr, "inexact overlaps #: %lld\n", forward - exact);
fprintf(stderr, "overlaps without large indels#: %lld\n", no_l_indel);
fprintf(stderr, "reverse overlaps #: %lld\n", reverse);
fprintf(stderr, "****************statistic for overlaps****************\n");
no_l_indel = forward = reverse = exact = strong = weak = 0;
for (i = 0; i < readNum; i++) {
forward += paf[i].length;
reverse += rev_paf[i].length;
for (j = 0; j < paf[i].length; j++) {
if (paf[i].buffer[j].el == 1) exact++;
if (paf[i].buffer[j].ml == 1) strong++;
if (paf[i].buffer[j].ml == 0) weak++;
if (paf[i].buffer[j].no_l_indel == 1) no_l_indel++;
}
}
fprintf(stderr, "[M::%s] # overlaps: %lld\n", __func__, forward);
fprintf(stderr, "[M::%s] # strong overlaps: %lld\n", __func__, strong);
fprintf(stderr, "[M::%s] # weak overlaps: %lld\n", __func__, weak);
fprintf(stderr, "[M::%s] # exact overlaps: %lld\n", __func__, exact); // this seems not right
fprintf(stderr, "[M::%s] # inexact overlaps: %lld\n", __func__, forward - exact);
fprintf(stderr, "[M::%s] # overlaps without large indels: %lld\n", __func__, no_l_indel);
fprintf(stderr, "[M::%s] # reverse overlaps: %lld\n", __func__, reverse);
}
void fill_chain(Fake_Cigar* chain, char* x_string, char* y_string, long long xBeg, long long yBeg,
long long x_readLen, long long y_readLen, Cigar_record* cigar, uint8_t* c2n)
{
@@ -1007,18 +989,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
}
finish_output_buffer();
ha_ovec_destroy(b);
pthread_mutex_lock(&statistics);
asm_opt.complete_threads++;
if(asm_opt.complete_threads == asm_opt.thread_num)
{
if(VERBOSE >= 1)
{
statistic(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
}
}
pthread_mutex_unlock(&statistics);
return NULL;
}
@@ -1222,6 +1192,8 @@ int ha_assemble(void)
clear_opt(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_overlap_and_correct(r);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> corrected reads for round %d\n", __func__, yak_realtime(), yak_cputime() / yak_realtime(), r + 1);
fprintf(stderr, "[M::%s] # bases: %lld; # corrected bases: %lld; # recorrected bases: %lld\n", __func__,
asm_opt.num_bases, asm_opt.num_corrected_bases, asm_opt.num_recorrected_bases);
}
Output_corrected_reads();
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> written corrected reads to disk\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
@@ -1229,6 +1201,7 @@ int ha_assemble(void)
clear_opt(&asm_opt, asm_opt.number_of_round);
ha_overlap_final();
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cputime() / yak_realtime());
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
Output_PAF();
trio_partition();
CommandLines.cpp
-2
View File
@@ -78,7 +78,6 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->number_of_round = 2;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
asm_opt->complete_threads = 0;
asm_opt->small_pop_bubble_size = 100000;
asm_opt->large_pop_bubble_size = 10000000;
asm_opt->min_drop_rate = 0.2;
@@ -103,7 +102,6 @@ void destory_opt(hifiasm_opt_t* asm_opt)
void clear_opt(hifiasm_opt_t* asm_opt, int round)
{
asm_opt->complete_threads = 0;
asm_opt->num_bases = 0;
asm_opt->num_corrected_bases = 0;
asm_opt->num_recorrected_bases = 0;
CommandLines.h
+1 -2
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r188"
#define HA_VERSION "0.3.0-dirty-r189"
#define VERBOSE 0
#define VERBOSE_GFA 0
@@ -30,7 +30,6 @@ typedef struct {
int number_of_round;
int adapterLen;
int clean_round;
int complete_threads;
int roundID;
int max_hang_Len;
int gap_fuzz;