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seperate purgeing and hom peak

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chhylp123
2021-07-25 11:23:06 -04:00
parent 6a043540b5
commit b14f894160
6 changed files with 87 additions and 22 deletions
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CommandLines.cpp
+17 -5
View File
@@ -21,7 +21,7 @@ static ko_longopt_t long_options[] = {
{ "max-od-final", ko_no_argument, 306 },
{ "ex-list", ko_required_argument, 307 },
{ "ex-iter", ko_required_argument, 308 },
{ "purge-cov", ko_required_argument, 309 },
{ "hom-cov", ko_required_argument, 309 },
{ "pri-range", ko_required_argument, 310 },
{ "lowQ", ko_required_argument, 312 },
{ "min-hist-cnt", ko_required_argument, 313 },
@@ -39,6 +39,7 @@ static ko_longopt_t long_options[] = {
{ "n-hap", ko_required_argument, 325 },
{ "n-weight", ko_required_argument, 326 },
{ "l-msjoin", ko_required_argument, 327 },
{ "purge-max", ko_required_argument, 328 },
{ 0, 0, 0 }
};
@@ -55,9 +56,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, "Options:\n");
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -o STR prefix of output files [%s]\n", asm_opt->output_file_name);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -t INT number of threads [%d]\n", asm_opt->thread_num);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " --version show version number\n");
fprintf(stderr, " Overlap/Error correction:\n");
fprintf(stderr, " -k INT k-mer length (must be <64) [%d]\n", asm_opt->k_mer_length);
@@ -68,12 +68,16 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -r INT round of correction [%d]\n", asm_opt->number_of_round);
fprintf(stderr, " Assembly:\n");
fprintf(stderr, " -a INT round of assembly cleaning [%d]\n", asm_opt->clean_round);
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -m INT pop bubbles of <INT in size in contig graphs [%lld]\n", asm_opt->large_pop_bubble_size);
fprintf(stderr, " -p INT pop bubbles of <INT in size in unitig graphs [%lld]\n", asm_opt->small_pop_bubble_size);
fprintf(stderr, " -n INT remove tip unitigs composed of <=INT reads [%d]\n", asm_opt->max_short_tip);
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
fprintf(stderr, " -i ignore saved read correction and overlaps\n");
fprintf(stderr, " -u disable post join contigs step which may improve N50\n");
fprintf(stderr, " --hom-cov INT\n");
fprintf(stderr, " homozygous read coverage [auto]\n");
fprintf(stderr, " --lowQ INT\n");
fprintf(stderr, " output contig regions with >=INT%% inconsistency in BED format; 0 to disable [%d]\n", asm_opt->bed_inconsist_rate);
fprintf(stderr, " --b-cov INT\n");
@@ -105,7 +109,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
asm_opt->purge_simi_rate_l2, asm_opt->purge_simi_rate_l3);
fprintf(stderr, " -O INT min number of overlapped reads for duplicate haplotigs [%d]\n",
asm_opt->purge_overlap_len);
fprintf(stderr, " --purge-cov INT\n");
fprintf(stderr, " --purge-max INT\n");
fprintf(stderr, " coverage upper bound of Purge-dups [auto]\n");
fprintf(stderr, " --n-hap INT\n");
fprintf(stderr, " number of haplotypes [%d]\n", asm_opt->polyploidy);
@@ -183,6 +187,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->recover_atg_cov_max = INT_MAX;
asm_opt->hom_global_coverage = -1;
asm_opt->hom_global_coverage_set = 0;
asm_opt->pur_global_coverage = -1;
asm_opt->bed_inconsist_rate = 70;
asm_opt->hic_inconsist_rate = 30;
///asm_opt->bub_mer_length = 3;
@@ -410,7 +415,13 @@ int check_option(hifiasm_opt_t* asm_opt)
if(asm_opt->hom_global_coverage < 0 && asm_opt->hom_global_coverage != -1)
{
fprintf(stderr, "[ERROR] purge duplication coverage threshold should be >= 0 (--purge-cov)\n");
fprintf(stderr, "[ERROR] homozygous read coverage should be >= 0 (--hom-cov)\n");
return 0;
}
if(asm_opt->pur_global_coverage < 0 && asm_opt->pur_global_coverage != -1)
{
fprintf(stderr, "[ERROR] purge duplication coverage threshold should be >= 0 (--purge-max)\n");
return 0;
}
@@ -663,6 +674,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 325) asm_opt->polyploidy = atoi(opt.arg);
else if (c == 326) asm_opt->n_weight = atoi(opt.arg);
else if (c == 327) asm_opt->misjoin_len = atol(opt.arg);
else if (c == 328) asm_opt->pur_global_coverage = atoi(opt.arg);
else if (c == 'l')
{ ///0: disable purge_dup; 1: purge containment; 2: purge overlap
asm_opt->purge_level_primary = asm_opt->purge_level_trio = atoi(opt.arg);
CommandLines.h
+2 -1
View File
@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.15.4-r348"
#define HA_VERSION "0.15.4-r349"
#define VERBOSE 0
@@ -77,6 +77,7 @@ typedef struct {
int recover_atg_cov_max;
int hom_global_coverage;
int hom_global_coverage_set;
int pur_global_coverage;
int bed_inconsist_rate;
int hic_inconsist_rate;
Overlaps.cpp
+4 -2
View File
@@ -16995,7 +16995,8 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_max = (asm_opt.hom_global_coverage_set?
(asm_opt.hom_global_coverage):(((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)));
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.85;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
@@ -24806,7 +24807,8 @@ uint32_t collect_p_trans, uint32_t collect_p_trans_f)
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_max = (asm_opt.hom_global_coverage_set?
(asm_opt.hom_global_coverage):(((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)));
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.85;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
Purge_Dups.cpp
+7 -2
View File
@@ -5267,9 +5267,14 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans, uint32_t colle
hap_alignment_struct_pip hap_buf;
long long k_mer_only, coverage_only;
if(asm_opt.hom_global_coverage != -1)
if(asm_opt.pur_global_coverage != -1)
{
hap_buf.cov_threshold = asm_opt.hom_global_coverage;
hap_buf.cov_threshold = asm_opt.pur_global_coverage;
}
else if(asm_opt.hom_global_coverage != -1)
{
hap_buf.cov_threshold = (asm_opt.hom_global_coverage_set?
(((double)asm_opt.hom_global_coverage)*((double)HOM_PEAK_RATE)):(asm_opt.hom_global_coverage));
}
else
{
hic.cpp
+45 -8
View File
@@ -43,6 +43,7 @@ KRADIX_SORT_INIT(u_trans_m, u_trans_t, u_trans_m_key, 8)
KRADIX_SORT_INIT(u_trans_occ, u_trans_t, u_trans_occ_key, member_size(u_trans_t, occ))
#define is_hom_hit(a) ((a).id == (uint64_t)-1)
#define HC_PT_MA 65
typedef struct {
kv_gg_status sg;
@@ -555,7 +556,9 @@ int write_hc_pt_index(ha_ug_index* idx, char* file_name)
free(gfa_name);
return 0;
}
uint64_t i = HC_PT_MA;
fwrite(&i, sizeof(i), 1, fp);
fwrite(&idx->uID_bits, sizeof(idx->uID_bits), 1, fp);
fwrite(&idx->uID_mode, sizeof(idx->uID_mode), 1, fp);
fwrite(&idx->pos_bits, sizeof(idx->pos_bits), 1, fp);
@@ -566,7 +569,6 @@ int write_hc_pt_index(ha_ug_index* idx, char* file_name)
fwrite(&idx->tot, sizeof(idx->tot), 1, fp);
fwrite(&idx->tot_pos, sizeof(idx->tot_pos), 1, fp);
uint64_t i = 0;
for (i = 0; i < idx->tot; i++)
{
fwrite(&idx->idx_buf[i].n, sizeof(idx->idx_buf[i].n), 1, fp);
@@ -596,7 +598,19 @@ int load_hc_pt_index(ha_ug_index** r_idx, ma_ug_t *ug, char* file_name)
return 0;
}
ha_ug_index* idx = NULL; CALLOC(idx, 1);
uint64_t i;
flag += fread(&i, sizeof(i), 1, fp);
if(i != HC_PT_MA)
{
free(gfa_name);
destory_hc_pt_index(idx);
free(idx);
(*r_idx) = NULL;
fclose(fp);
fprintf(stderr, "[M::%s::] ==> Renew Hi-C index\n", __func__);
return 0;
}
flag += fread(&idx->uID_bits, sizeof(idx->uID_bits), 1, fp);
flag += fread(&idx->uID_mode, sizeof(idx->uID_mode), 1, fp);
flag += fread(&idx->pos_bits, sizeof(idx->pos_bits), 1, fp);
@@ -607,7 +621,7 @@ int load_hc_pt_index(ha_ug_index** r_idx, ma_ug_t *ug, char* file_name)
flag += fread(&idx->tot, sizeof(idx->tot), 1, fp);
flag += fread(&idx->tot_pos, sizeof(idx->tot_pos), 1, fp);
MALLOC(idx->idx_buf, idx->tot);
uint64_t i = 0;
for (i = 0; i < idx->tot; i++)
{
flag += fread(&idx->idx_buf[i].n, sizeof(idx->idx_buf[i].n), 1, fp);
@@ -876,6 +890,14 @@ ha_ug_index* build_unitig_index(ma_ug_t *ug, int k, uint64_t up_occ, uint64_t lo
fprintf(stderr, "[M::%s::%.3f] ==> Sorting pos\n", __func__, yak_realtime()-beg_time);
fprintf(stderr, "[M::%s::%.3f] ==> HiC index has been built\n", __func__, yak_realtime()-index_time);
uint64_t i;
for (i = 0; i < idx->tot; i++)
{
kv_destroy(pl.cnt[i].a);
kv_destroy(pl.buf[i].a);
}
free(pl.cnt); free(pl.buf);
return idx;
}
@@ -4043,6 +4065,7 @@ void update_containment_distance(asg_t *sg, kv_u_trans_t *ta, hc_links* link)
}
kv_destroy(buf.a);
free(uc_idx);
}
@@ -4877,7 +4900,12 @@ int load_hc_hits(kvec_pe_hit* hits, ma_ug_t* ug, const char *fn)
FILE* fp = NULL;
fp = fopen(buf, "r");
if(!fp) return 0;
if(!fp)
{
free(buf);
return 0;
}
kv_init(hits->a);
flag += fread(&hits->a.n, sizeof(hits->a.n), 1, fp);
@@ -9506,11 +9534,20 @@ H_partition* hap, int8_t *s, mc_gg_status *sa, trans_idx* dis)
if((buf.a[k]&1) == 1) f_idx = k;
}
buf.n = MIN(r_idx, f_idx);
trans_p_t* p = NULL;
dis->n = 0;
uint64_t bin_size = MIN(2250, buf.n>>8), m;
if(bin_size == 0)
{
for (i = 8; i > 0; i--)
{
bin_size = buf.n>>i;
if(bin_size > 0) break;
}
if(bin_size == 0) bin_size = buf.n;
}
i = 0;
while (i < buf.n)
{
@@ -9603,7 +9640,7 @@ H_partition* hap, int8_t *s, mc_gg_status *sa, trans_idx* dis)
dis->a[i].end += ((dis->a[i+1].beg - dis->a[i].end)/2);
dis->a[i+1].beg = dis->a[i].end;
}
// for (i = 0; i < dis->n; i++)
// {
// if(i > 0 && dis->a[i].beg != dis->a[i-1].end) fprintf(stderr, "ERROR: dis->a[i].beg: %lu, dis->a[i-1].end: %lu\n", dis->a[i].beg, dis->a[i-1].end);
@@ -9617,7 +9654,7 @@ H_partition* hap, int8_t *s, mc_gg_status *sa, trans_idx* dis)
dis->max = dis->a[dis->n-1].end;
if(idx->a < 0) idx->a = 0;
if(idx->a == 0)
@@ -16166,7 +16203,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
idx->hap_cnt = asm_opt.hap_occ;
kv_init(sl.hits.a); kv_init(sl.hits.idx); kv_init(sl.hits.occ);
if(!load_hc_hits(&sl.hits, idx->ug, asm_opt.output_file_name))
{
alignment_worker_pipeline(&sl, fn1, fn2);
@@ -16448,7 +16485,7 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt,
else hic_short_align_poy(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt);
destory_hc_pt_index(ug_index);
destory_hc_pt_index(ug_index);free(ug_index);
}
khashl.h
+12 -4
View File
@@ -136,25 +136,33 @@ static kh_inline khint_t __kh_h2b(khint_t hash, khint_t bits) { return hash * 26
#define __KHASHL_IMPL_S_L(SCOPE, HType, prefix, khkey_t) \
SCOPE khint_t prefix##_save(HType *h, FILE* fp) { \
if (!h) return 0; \
uint8_t ff; \
khint_t n_buckets = (h->keys? 1U<<h->bits : 0U); \
fwrite(&n_buckets, sizeof(n_buckets), 1, fp); \
fwrite(&h->bits, sizeof(h->bits), 1, fp); \
fwrite(&h->count, sizeof(h->count), 1, fp); \
fwrite(h->used, sizeof(khint32_t), __kh_fsize(n_buckets), fp); \
fwrite(h->keys, sizeof(khkey_t), n_buckets, fp); \
ff = h->used? 1:0; fwrite(&ff, sizeof(ff), 1, fp); \
if(ff) fwrite(h->used, sizeof(khint32_t), __kh_fsize(n_buckets), fp); \
ff = h->keys? 1:0; fwrite(&ff, sizeof(ff), 1, fp); \
if(ff) fwrite(h->keys, sizeof(khkey_t), n_buckets, fp); \
return 1; \
} \
SCOPE khint_t prefix##_load(HType **h, FILE* fp) { \
(*h) = prefix##_init(); \
khint_t n_buckets; \
uint64_t flag = 0;\
uint8_t ff; \
flag += fread(&n_buckets, sizeof(n_buckets), 1, fp); \
flag += fread(&(*h)->bits, sizeof((*h)->bits), 1, fp); \
flag += fread(&(*h)->count, sizeof((*h)->count), 1, fp); \
flag += fread(&ff, sizeof(ff), 1, fp); \
if(ff) {\
(*h)->used = (khint32_t*)kmalloc(__kh_fsize(n_buckets) * sizeof(khint32_t)); \
flag += fread((*h)->used, sizeof(khint32_t), __kh_fsize(n_buckets), fp); }\
flag += fread(&ff, sizeof(ff), 1, fp); \
if(ff) {\
(*h)->keys = (khkey_t*)kmalloc(n_buckets * sizeof(khkey_t)); \
flag += fread((*h)->used, sizeof(khint32_t), __kh_fsize(n_buckets), fp); \
flag += fread((*h)->keys, sizeof(khkey_t), n_buckets, fp); \
flag += fread((*h)->keys, sizeof(khkey_t), n_buckets, fp); }\
return 1; \
} \