xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-25 16:28:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r201: automatically adjust -N

Browse Source
This commit is contained in:
Heng Li
2020-04-05 22:43:01 -04:00
parent 3773610532
commit adbc65feda
5 changed files with 43 additions and 33 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Assembly.cpp
+15 -11
View File
@@ -382,7 +382,7 @@ typedef struct {
overlap_region_alloc olist;
ha_abuf_t *ab;
// error correction related buffers
int64_t num_read_base, num_correct_base, num_recorrect_base, mem_buf;
int64_t num_read_base, num_correct_base, num_recorrect_base;
Cigar_record cigar1;
Graph POA_Graph;
Graph DAGCon;
@@ -626,7 +626,7 @@ void Output_corrected_reads()
void ha_overlap_and_correct(int round)
{
int i;
int i, hom_cov;
ha_ovec_buf_t **b;
ha_ecsave_buf_t *e;
@@ -634,7 +634,9 @@ void ha_overlap_and_correct(int round)
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(0);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF); // build the index
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF, &hom_cov); // build the index
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
if (asm_opt.required_read_name)
kt_for(asm_opt.thread_num, worker_ovec_related_reads, b, R_INF.total_reads);
else
@@ -647,7 +649,7 @@ void ha_overlap_and_correct(int round)
asm_opt.num_bases += b[i]->num_read_base;
asm_opt.num_corrected_bases += b[i]->num_correct_base;
asm_opt.num_recorrected_bases += b[i]->num_recorrect_base;
asm_opt.mem_buf += b[i]->mem_buf;
asm_opt.mem_buf += ha_ovec_mem(b[i]);
ha_ovec_destroy(b[i]);
}
free(b);
@@ -1135,12 +1137,12 @@ long long readNum, long long rescue_threshold, float cluster_threshold)
void ha_overlap_final(void)
{
int i;
int i, hom_cov;
ha_ovec_buf_t **b;
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(1);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF); // build the index
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF, &hom_cov); // build the index
kt_for(asm_opt.thread_num, worker_ov_final, b, R_INF.total_reads);
ha_pt_destroy(ha_idx);
ha_idx = 0;
@@ -1151,19 +1153,21 @@ void ha_overlap_final(void)
int ha_assemble(void)
{
int r, ovlp_loaded = 0;
int r, hom_cov = -1, ovlp_loaded = 0;
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
}
if (!ovlp_loaded) {
// construct hash table for high occurrence k-mers
if (!asm_opt.no_kmer_flt)
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF);
if (!asm_opt.no_kmer_flt) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov);
ha_opt_update_cov(&asm_opt, hom_cov);
}
// error correction
assert(asm_opt.number_of_round > 0);
for (r = 0; r < asm_opt.number_of_round; ++r) {
clear_opt(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_overlap_and_correct(r);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> corrected reads for round %d\n", __func__, yak_realtime(),
yak_cpu_usage(), yak_peakrss_in_gb(), r + 1);
@@ -1174,7 +1178,7 @@ int ha_assemble(void)
//Output_corrected_reads();
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> written corrected reads to disk\n", __func__, yak_realtime(), yak_cpu_usage());
// overlap between corrected reads
clear_opt(&asm_opt, asm_opt.number_of_round);
ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
ha_overlap_final();
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(),
yak_cpu_usage(), yak_peakrss_in_gb());