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@chhylp123
chhylp123 committed Sep 26, 2021
1 parent ed814ab commit 7dd4a84
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Showing 13 changed files with 2,747 additions and 61 deletions.
4 changes: 3 additions & 1 deletion CommandLines.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->hic_enzymes = NULL;
asm_opt->hic_reads[0] = NULL;
asm_opt->hic_reads[1] = NULL;
asm_opt->fn_bin_poy = NULL;
asm_opt->ar = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 51;
Expand Down Expand Up @@ -654,7 +655,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)

int c;

while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:l:s:O:eu", long_options)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:5:l:s:O:eu", long_options)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
Expand Down Expand Up @@ -684,6 +685,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == '2' || c == 'M') asm_opt->fn_bin_yak[1] = opt.arg;
else if (c == '3') asm_opt->fn_bin_list[0] = opt.arg;
else if (c == '4') asm_opt->fn_bin_list[1] = opt.arg;
else if (c == '5') asm_opt->fn_bin_poy = opt.arg;
else if (c == 'x') asm_opt->max_drop_rate = atof(opt.arg);
else if (c == 'y') asm_opt->min_drop_rate = atof(opt.arg);
else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);
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 @@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>

#define HA_VERSION "0.16.1-r375"
#define HA_VERSION "0.16.1-r377"

#define VERBOSE 0

Expand Down Expand Up @@ -38,6 +38,7 @@ typedef struct {
char* required_read_name;
char *fn_bin_yak[2];
char *fn_bin_list[2];
char *fn_bin_poy;
char *extract_list;
enzyme *hic_reads[2];
enzyme *hic_enzymes;
Expand Down
3 changes: 2 additions & 1 deletion Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ INCLUDES=
OBJS= CommandLines.o Process_Read.o Assembly.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o Purge_Dups.o \
htab.o hist.o sketch.o anchor.o extract.o sys.o ksw2_extz2_sse.o hic.o rcut.o horder.o \
tovlp.o inter.o
tovlp.o inter.o kalloc.o
EXE= hifiasm
LIBS= -lz -lpthread -lm

Expand Down Expand Up @@ -77,3 +77,4 @@ rcut.o: rcut.h
horder.o: horder.h
tovlp.o: tovlp.h
inter.o: inter.h
kalloc.o: kalloc.h
127 changes: 106 additions & 21 deletions Overlaps.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13090,6 +13090,61 @@ void hic_clean(asg_t* read_g)
kv_destroy(ax);
}

void update_poly_trio(uint32_t mm, uint32_t *hapS, uint32_t rn)
{
uint32_t i;
for (i = 0; i < rn; i++) {
if(R_INF.trio_flag[i] == DROP) continue;
R_INF.trio_flag[i] = AMBIGU;
if(!hapS[i]) continue;
R_INF.trio_flag[i] = (hapS[i]&mm?FATHER:MOTHER);
}
}
void debug_hapS(uint32_t *hapS, uint32_t rn)
{
uint32_t i, p, tot, nt, max_tot = 0, *occ = NULL, *freq = NULL;
for (i = 0; i < rn; i++) {
for (p = hapS[i], tot = 0; p; p>>=1, tot++);
max_tot = MAX(max_tot, tot);
}
fprintf(stderr, "[M::%s:] ==> %u haplotypes in total\n", __func__, max_tot);
if(max_tot){
CALLOC(occ, max_tot+1);
CALLOC(freq, max_tot+1);
for (i = 0; i < rn; i++) {
for (p = hapS[i], tot = nt = 0; p; p>>=1, tot++){
if(p&1) occ[tot+1]++, nt++;
}
freq[nt]++;
}
for (i = 1; i <= max_tot; i++) {
fprintf(stderr, "[M::%s:] ==> # reads in hap%u: %u\n", __func__, i, occ[i]);
}
for (i = 0; i <= max_tot; i++) {
fprintf(stderr, "[M::%s:] ==> # reads within %u haplotypes: %u\n", __func__, i, freq[i]);
}
free(occ); free(freq);
}
}
void output_poly_trio(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
bub_label_t* b_mask_t, uint32_t hapN)
{
uint32_t i;
uint32_t *hapS = ha_polybin_list(&asm_opt);
// debug_hapS(hapS, sg->n_seq);
char *fp = NULL; MALLOC(fp, 100);
for (i = 0; i < hapN; i++){
update_poly_trio(1<<i, hapS, sg->n_seq);
sprintf(fp, "hap%u", i+1);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, tipsLen, tip_drop_ratio,
stops_threshold, ruIndex, chimeric_rate, drop_ratio, max_hang, min_ovlp, is_bench, b_mask_t, fp);
}
free(fp); free(hapS);
}


void output_contig_graph_alternative(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp);
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g);
Expand Down Expand Up @@ -13212,9 +13267,9 @@ long long gap_fuzz, bub_label_t* b_mask_t)
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);

ug_fa = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL);
ug_mo = output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, rhits?1:0, b_mask_t, NULL);
if(rhits)
{
ha_aware_order(rhits, sg, ug_fa, ug_mo, cov?&(cov->t_ch->k_trans):&(t_ch->k_trans), &opt, 3);
Expand Down Expand Up @@ -13320,9 +13375,9 @@ long long gap_fuzz, bub_label_t* b_mask_t)
reduce_hamming_error(sg, sources, coverage_cut, max_hang, min_ovlp, gap_fuzz);

output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
}

void set_trio_flag_by_cov(ma_ug_t *ug, asg_t *read_g, hap_cov_t *cov)
Expand Down Expand Up @@ -14117,9 +14172,9 @@ bub_label_t* b_mask_t)
kv_destroy(new_rtg_edges.a);

output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t, NULL);
}

ma_ug_t* merge_utg(ma_ug_t **dest, ma_ug_t **src)
Expand Down Expand Up @@ -14186,11 +14241,11 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, bub_label_t*
{
ma_ug_t *ug_1 = output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex,
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL);

ma_ug_t *ug_2 = output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources,
reverse_sources, tipsLen, tip_drop_ratio, stops_threshold, ruIndex,
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t);
chimeric_rate, drop_ratio, max_hang, min_ovlp, 1, b_mask_t, NULL);
fprintf(stderr, "ug_1->u.n: %u, ug_2->u.n: %u\n", (uint32_t)ug_1->u.n, (uint32_t)ug_2->u.n);
ma_ug_t *ug = merge_utg(&ug_1, &ug_2);
fprintf(stderr, "ug->u.n: %u\n", (uint32_t)ug->u.n);
Expand Down Expand Up @@ -15258,10 +15313,7 @@ hap_cov_t *cov, utg_trans_t *o)
uint8_t if_primary_unitig(ma_utg_t* u, asg_t* read_g, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
{
if(asm_opt.recover_atg_cov_min < 0 || asm_opt.recover_atg_cov_max < 0)
{
return 0;
}
if(asm_opt.recover_atg_cov_min < 0 || asm_opt.recover_atg_cov_max < 0) return 0;
long long R_bases = 0, C_bases = 0, C_bases_primary = 0, C_bases_alter = 0;
long long total_C_bases = 0, total_C_bases_primary = 0;
uint32_t available_reads = 0, k, j, rId, tn, is_Unitig;
Expand Down Expand Up @@ -15979,7 +16031,7 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex, cov->is_r_het, 2);
}

///print_debug_gfa(read_g, ug, coverage_cut, "debug_dups", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
// print_debug_gfa(read_g, ug, coverage_cut, "debug_dups", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, cov->is_r_het, trio_flag, drop_ratio);
drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex, cov->is_r_het);
Expand Down Expand Up @@ -16870,6 +16922,31 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex)
return u_flag;
}

void purge_dump(ma_ug_t* ug)
{
asg_t* nsg = ug->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId;
ma_utg_t *u = NULL;
for (v = 0; v < n_vtx; ++v) {
if (nsg->seq[v].del) continue;
u = &((ug)->u.a[v]);
if(u->m == 0) continue;
for (k = 0; k < u->n; k++){
rId = u->a[k]>>33;
if(R_INF.trio_flag[rId] != AMBIGU && R_INF.trio_flag[rId] != DROP) break;
}
if(k >= u->n){
if(u->m != 0){
u->circ = u->end = u->len = u->m = u->n = u->start = 0;
free(u->a);
u->a = NULL;
}
asg_seq_del(nsg, v);
}
}
asg_cleanup(nsg);
}


void adjust_utg_by_trio(ma_ug_t **ug, asg_t* read_g, uint8_t flag, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
Expand Down Expand Up @@ -16974,6 +17051,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
set_drop_trio_flag(*ug);
destory_hap_cov_t(&cov);

// purge_dump(*ug);
renew_utg(ug, read_g, new_rtg_edges);
}

Expand All @@ -16999,10 +17077,11 @@ int debug_untig_length(ma_ug_t *g, uint32_t tipsLen, const char* name)
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t)
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t,
char *f_prefix)
{
char* gfa_name = (char*)malloc(strlen(output_file_name)+100);
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.gfa", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
FILE* output_file = NULL;
if(is_bench == 0) output_file = fopen(gfa_name, "w");

Expand Down Expand Up @@ -17043,13 +17122,13 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench,
ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, (flag==FATHER?"h1tg":"h2tg"), output_file);
fclose(output_file);

sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.noseq.gfa", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
output_file = fopen(gfa_name, "w");
ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, (flag==FATHER?"h1tg":"h2tg"), output_file);
fclose(output_file);
if(asm_opt.bed_inconsist_rate != 0)
{
sprintf(gfa_name, "%s.%s.p_ctg.lowQ.bed", output_file_name, (flag==FATHER?"hap1":"hap2"));
sprintf(gfa_name, "%s.%s.p_ctg.lowQ.bed", output_file_name, f_prefix?f_prefix:(flag==FATHER?"hap1":"hap2"));
output_file = fopen(gfa_name, "w");
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.bed_inconsist_rate, (flag==FATHER?"h1tg":"h2tg"), output_file, NULL);
Expand Down Expand Up @@ -30888,8 +30967,14 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex);
debug_gfa:;
}

if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))

if(asm_opt.fn_bin_poy)
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_poly_trio(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, asm_opt.polyploidy);
}
else if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
benchmark_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
Expand All @@ -30900,10 +30985,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
if(asm_opt.flag & HA_F_PARTITION) asm_opt.flag -= HA_F_PARTITION;
output_trio_unitig_graph(sg, coverage_cut, o_file, FATHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, NULL);
output_trio_unitig_graph(sg, coverage_cut, o_file, MOTHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t, NULL);
}
else if(ha_opt_hic(&asm_opt))
{
Expand Down
2 changes: 1 addition & 1 deletion Overlaps.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -913,7 +913,7 @@ ma_ug_t* copy_untig_graph(ma_ug_t *src);
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex,
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t);
float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t, char *f_prefix);
asg_t* copy_read_graph(asg_t *src);
ma_ug_t *ma_ug_gen(asg_t *g);
void ma_ug_destroy(ma_ug_t *ug);
Expand Down
77 changes: 77 additions & 0 deletions Trio.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -349,6 +349,83 @@ static void ha_triobin_list(const hifiasm_opt_t *opt)
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads with external lists\n", __func__, yak_realtime(), yak_cpu_usage());
}

inline void phrase_hstatus(char *s, char **rname, uint32_t *hid)
{
char *p = NULL, *id = NULL; *rname = NULL; *hid = (uint32_t)-1;
uint32_t tot;
for (p = s, tot = 0; *p; ++p){
if (*p == '\t' || *p == ' '){
*p = 0;
if(!tot) *rname = p+1;
else break;
tot++;
}
}
for (p = s, tot = 0; *p; ++p){
if (*p == '_') id = p + 1;
}
*hid = atoi(id);
}

uint32_t *ha_polybin_list(const hifiasm_opt_t *opt)
{
int64_t i;
khint_t k;
cstr_ht_t *h;
assert(R_INF.total_reads < (uint32_t)-1);
h = cstr_ht_init();
for (i = 0; i < (int64_t)R_INF.total_reads; ++i) {
int absent;
char *str = (char*)calloc(Get_NAME_LENGTH(R_INF, i) + 1, 1);
strncpy(str, Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i));
k = cstr_ht_put(h, str, &absent);
if (absent) kh_val(h, k) = i;
}
fprintf(stderr, "[M::%s::%.3f*%.2f] created the hash table for read names\n", __func__, yak_realtime(), yak_cpu_usage());

gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
char *rname = NULL;
uint32_t hid, *ss = NULL;
int dret;
int64_t n_tot = 0, n_bin = 0;
fp = gzopen(opt->fn_bin_poy, "r");
if (fp == 0) {
fprintf(stderr, "ERROR: failed to open file '%s'\n", opt->fn_bin_poy);
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
cstr_ht_destroy(h);
return NULL;
}
CALLOC(ss, R_INF.total_reads);
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
khint_t k; ++n_tot;
phrase_hstatus(str.s, &rname, &hid);
if((!(*rname)) || hid == (uint32_t)-1) {
fprintf(stderr, "ERROR: wrong hap status\n");
continue;
}
k = cstr_ht_get(h, rname);
if (k != kh_end(h)) {
ss[kh_val(h, k)] |= (((uint32_t)1)<<(hid-1));
++n_bin;
}
}
free(str.s);
ks_destroy(ks);
gzclose(fp);

for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
cstr_ht_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads with external lists\n", __func__, yak_realtime(), yak_cpu_usage());
return ss;
}

void ha_triobin(const hifiasm_opt_t *opt)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));
Expand Down
1 change: 1 addition & 0 deletions htab.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,7 @@ double yak_peakrss_in_gb(void);
double yak_cpu_usage(void);

void ha_triobin(const hifiasm_opt_t *opt);
uint32_t *ha_polybin_list(const hifiasm_opt_t *opt);

void mz1_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, ha_pt_t *pt, int min_freq, int32_t dp_min_len, float dp_e, st_mt_t *mt, int32_t ws, int32_t is_unique);
void mz2_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mzl_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, ha_pt_t *pt, int min_freq, int32_t dp_min_len, float dp_e, st_mt_t *mt, int32_t ws, int32_t is_unique);
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