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0.20.0-r631
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@chhylp123
chhylp123 committed Oct 9, 2024
1 parent d5f8a8a commit e8b1856
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Showing 14 changed files with 8,025 additions and 671 deletions.
119 changes: 57 additions & 62 deletions Assembly.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -970,86 +970,57 @@ void prt_dbg_rs(FILE *fp, Debug_reads* x, uint64_t round)
destory_UC_Read(&g_read);
}


void ha_ec(int64_t round)
void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t *tot_e)
{
int i, hom_cov, het_cov, r_out = 0;
ec_ovec_buf_t *b = NULL;
ha_ecsave_buf_t *e = NULL;
ha_flt_tab_hp = ha_idx_hp = NULL;
int hom_cov, het_cov, r_out = 0;
ha_flt_tab_hp = ha_idx_hp = NULL; (*tot_b) = (*tot_e) = 0;

if((ha_idx == NULL)&&(asm_opt.flag & HA_F_VERBOSE_GFA)&&(round == asm_opt.number_of_round - 1)) r_out = 1;

if(asm_opt.required_read_name) init_Debug_reads(&R_INF_FLAG, asm_opt.required_read_name); // for debugging only
// overlap and correct reads
b = gen_ec_ovec_buf_t(asm_opt.thread_num, 0, (round == asm_opt.number_of_round - 1));
// CALLOC(b, asm_opt.thread_num);
// for (i = 0; i < asm_opt.thread_num; ++i)
// b[i] = ha_ovec_init(0, (round == asm_opt.number_of_round - 1),0);


if(ha_idx) hom_cov = asm_opt.hom_cov;
if(ha_idx == NULL) ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
if(ha_idx == NULL) {
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
}
///debug_adapter(&asm_opt, &R_INF);
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
het_cnt = NULL;
if(round == asm_opt.number_of_round-1 && asm_opt.is_dbg_het_cnt) CALLOC(het_cnt, R_INF.total_reads);

/**
// fprintf(stderr, "[M::%s-start]\n", __func__);
if (asm_opt.required_read_name)
kt_for(asm_opt.thread_num, worker_ovec_related_reads, b, R_INF.total_reads);
else
kt_for(asm_opt.thread_num, worker_ovec, b, R_INF.total_reads);///debug_for_fix
// fprintf(stderr, "[M::%s-end]\n", __func__);
**/
cal_ec_multiple(b, asm_opt.thread_num, R_INF.total_reads);
// kt_for(asm_opt.thread_num, worker_hap_ec, b, R_INF.total_reads);///debug_for_fix

if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
ha_pt_destroy(ha_idx);
ha_idx = NULL;

cal_ec_r(asm_opt.thread_num, round, num_pround, R_INF.total_reads, (round == (asm_opt.number_of_round-1))?1:0, tot_b, tot_e);

// exit(1);

// if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
if(des_idx) {
ha_pt_destroy(ha_idx); ha_idx = NULL;
}


if(het_cnt) {
print_het_cnt_log(het_cnt); free(het_cnt); het_cnt = NULL;
}

/**
// collect statistics
for (i = 0; i < asm_opt.thread_num; ++i) {
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 += ha_ovec_mem(b[i], NULL);
ha_ovec_destroy(b[i]);
}
free(b);
**/
destroy_ec_ovec_buf_t(b);
exit(1);
// exit(1);


if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r0, &R_INF_FLAG, 0); // for debugging only

// save corrected reads to R_INF
CALLOC(e, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i) {
init_UC_Read(&e[i].g_read);
e[i].first_round_read_size = e[i].second_round_read_size = 50000;
CALLOC(e[i].first_round_read, e[i].first_round_read_size);
CALLOC(e[i].second_round_read, e[i].second_round_read_size);
}
kt_for(asm_opt.thread_num, worker_ec_save, e, R_INF.total_reads);
for (i = 0; i < asm_opt.thread_num; ++i) {
destory_UC_Read(&e[i].g_read);
free(e[i].first_round_read);
free(e[i].second_round_read);
}
free(e);
// sl_ec_r(asm_opt.thread_num, R_INF.total_reads);

if (asm_opt.required_read_name) prt_dbg_rs(R_INF_FLAG.fp_r1, &R_INF_FLAG, 1); // for debugging only
if (asm_opt.required_read_name) destory_Debug_reads(&R_INF_FLAG), exit(0); // for debugging only
///debug_print_pob_regions();

// Output_corrected_reads();

// exit(1);
}


Expand Down Expand Up @@ -1927,6 +1898,25 @@ void ha_overlap_final(void)
asm_opt.het_cov = het_cov;
}

void ha_ec_ff(int renew_idx)
{
int hom_cov, het_cov;
ha_flt_tab_hp = ha_idx_hp = NULL;

if(ha_idx && renew_idx) {
ha_pt_destroy(ha_idx); ha_idx = NULL;
}

if(!ha_idx) {
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
}

cal_ov_r(asm_opt.thread_num, R_INF.total_reads, renew_idx);

ha_pt_destroy(ha_idx); ha_idx = NULL;
}

static void worker_ov_utg(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
Expand Down Expand Up @@ -2016,7 +2006,7 @@ int ha_assemble(void)
// debug_mc_gg_t(MC_NAME, 0, 0);
// quick_debug_phasing(MC_NAME);
extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
int r, hom_cov = -1, ovlp_loaded = 0;
int r, hom_cov = -1, ovlp_loaded = 0; uint64_t tot_b, tot_e;
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());
Expand All @@ -2042,24 +2032,29 @@ int ha_assemble(void)
assert(asm_opt.number_of_round > 0);
for (r = ha_idx?asm_opt.number_of_round-1:0; r < asm_opt.number_of_round; ++r) {
ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
tot_b = tot_e = 0;
// ha_overlap_and_correct(r);
ha_ec(r);
ha_ec(r, asm_opt.number_of_pround, (r<asm_opt.number_of_round-1)?1:0, &tot_b, &tot_e);
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);
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);
fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
fprintf(stderr, "[M::%s] # bases: %lu; # corrected bases: %lu\n", __func__, tot_b, tot_e);
// 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);
// fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
}
if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
// overlap between corrected reads
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());
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
// ha_overlap_final();
ha_ec_ff(1/**0**/);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
// fprintf(stderr, "\n[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
// ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
ha_triobin(&asm_opt);

// exit(1);
}
if(ovlp_loaded == 2) ovlp_loaded = 0;
ha_opt_update_cov_min(&asm_opt, asm_opt.hom_cov, MIN_N_CHAIN);
Expand Down
5 changes: 3 additions & 2 deletions CommandLines.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@ static ko_longopt_t long_options[] = {
{ "write-paf", ko_no_argument, 302 },
{ "write-ec", ko_no_argument, 303 },
{ "skip-triobin", ko_no_argument, 304 },
{ "max-od-ec", ko_no_argument, 305 },
{ "max-od-final", ko_no_argument, 306 },
{ "max-od-ec", ko_required_argument, 305 },
{ "max-od-final", ko_required_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "hom-cov", ko_required_argument, 309 },
Expand Down Expand Up @@ -249,6 +249,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->load_index_from_disk = 1;
asm_opt->write_index_to_disk = 1;
asm_opt->number_of_round = 3;
asm_opt->number_of_pround = 0/**3**/;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
///asm_opt->small_pop_bubble_size = 100000;
Expand Down
3 changes: 2 additions & 1 deletion CommandLines.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>

#define HA_VERSION "0.19.9-r616"
#define HA_VERSION "0.20.0-r631"

#define VERBOSE 0

Expand Down Expand Up @@ -74,6 +74,7 @@ typedef struct {
int load_index_from_disk;
int write_index_to_disk;
int number_of_round;
int number_of_pround;
int adapterLen;
int clean_round;
int roundID;
Expand Down
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