xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-24 04:08:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r181: limit the max number of chains

Browse Source
This commit is contained in:
Heng Li
2020-04-02 21:55:00 -04:00
parent 3838482851
commit 968b4caef9
9 changed files with 65 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Assembly.cpp
+4 -4
View File
@@ -10,7 +10,7 @@
#include "Output.h"
#include "htab.h"
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain);
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain);
All_reads R_INF;
pthread_mutex_t statistics;
@@ -423,7 +423,7 @@ void* Overlap_calculate_heap_merge(void* arg)
{
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.02, 1);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.02, 1);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.02, asm_opt.max_n_chain, 1);
clear_Cigar_record(&current_cigar);
clear_Round2_alignment(&second_round);
@@ -543,7 +543,7 @@ void* Output_related_reads(void* arg)
{
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.02, 1);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.02, 1);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.02, asm_opt.max_n_chain, 1);
fprintf(stderr, ">%.*s\n", (int)Get_NAME_LENGTH((R_INF), i),
Get_NAME((R_INF), i));
@@ -1109,7 +1109,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
{
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.001, 0);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.001, asm_opt.max_n_chain, 0);
/**
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,
CommandLines.cpp
+3 -1
View File
@@ -69,6 +69,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->high_factor = 5.0f;
asm_opt->no_HPC = 0;
asm_opt->no_kmer_flt = 0;
asm_opt->max_n_chain = 1000;
asm_opt->k_mer_min_freq = 3;
asm_opt->k_mer_max_freq = 66;
asm_opt->load_index_from_disk = 1;
@@ -300,7 +301,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
int c;
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:F", 0)) >= 0) {
while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:", 0)) >= 0) {
if (c == 'h')
{
Print_H(asm_opt);
@@ -321,6 +322,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
else if (c == 'w') asm_opt->mz_win = atoi(opt.arg);
else if (c == 'D') asm_opt->high_factor = atof(opt.arg);
else if (c == 'F') asm_opt->no_kmer_flt = 1;
else if (c == 'N') asm_opt->max_n_chain = atoi(opt.arg);
else if (c == 'a') asm_opt->clean_round = atoi(opt.arg);
else if (c == 'z') asm_opt->adapterLen = atoi(opt.arg);
else if (c == 'b') asm_opt->required_read_name = opt.arg;
CommandLines.h
+2 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.3.0-dirty-r179"
#define HA_VERSION "0.3.0-dirty-r181"
#define VERBOSE 0
#define VERBOSE_GFA 0
@@ -22,6 +22,7 @@ typedef struct {
float high_factor;
int no_HPC;
int no_kmer_flt;
int max_n_chain;
int k_mer_min_freq;
int k_mer_max_freq;
int load_index_from_disk;
Hash_Table.cpp
+2 -4
View File
@@ -816,12 +816,10 @@ void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift)
void resize_fake_cigar(Fake_Cigar* x, uint64_t size)
{
if(size > x->size)
{
if (size > x->size) {
x->size = size;
x->buffer = (uint64_t*)realloc(x->buffer, sizeof(uint64_t) * x->size);
REALLOC(x->buffer, x->size);
}
x->length = 0;
}
Hash_Table.h
+8 -8
View File
@@ -67,15 +67,15 @@ typedef struct
typedef struct
{
window_list* buffer;
long long length;
long long size;
int32_t length;
int32_t size;
} window_list_alloc;
typedef struct
{
uint64_t* buffer;
uint64_t length;
uint64_t size;
uint32_t length;
uint32_t size;
} Fake_Cigar;
typedef struct
@@ -96,12 +96,12 @@ typedef struct
uint32_t align_length;
uint8_t is_match;
uint8_t without_large_indel;
int8_t strong;
uint32_t non_homopolymer_errors;
window_list* w_list;
uint64_t w_list_size;
uint64_t w_list_length;
int8_t strong;
uint32_t w_list_size;
uint32_t w_list_length;
Fake_Cigar f_cigar;
window_list_alloc boundary_cigars;
@@ -180,7 +180,7 @@ static inline long long y_start_offset(long long x_start, Fake_Cigar* o)
if(i == 0 || i == (long long)o->length)
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
exit(0);
}
Overlaps.cpp
+8 -8
View File
@@ -4333,7 +4333,7 @@ uint32_t startNode, uint32_t endNode)
}
else
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
}
if(asg_arc_a(g, N_list[2])[0].v == (N_list[0]^1))
@@ -4346,7 +4346,7 @@ uint32_t startNode, uint32_t endNode)
}
else
{
fprintf(stderr, "ERROR\n");
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
}
if(N_list[3] != N_list[4])
@@ -9028,7 +9028,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
break;
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
av = asg_arc_a(read_g, v);
nv = asg_arc_n(read_g, v);
@@ -9042,7 +9042,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
}
if(k == nv) fprintf(stderr, "ERROR\n");
if(k == nv) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
if(pE->el == 1 && aE->el == 1) continue;
@@ -9123,7 +9123,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
l = asg_arc_len(t_f);
}
if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
if(l == (uint32_t)-1) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
/*******************************for debug************************************/
@@ -9172,7 +9172,7 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp)
}
l = asg_arc_len(t_f);
}
if(l == (uint32_t)-1) fprintf(stderr, "ERROR\n");
if(l == (uint32_t)-1) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
/*******************************for debug************************************/
@@ -19547,7 +19547,7 @@ void merge_ug_nodes(ma_ug_t *ug, asg_t* read_g, kvec_t_u64_warp* array)
if(aw[i].del) continue;
if(aw[i].v == (v^1)) break;
}
if(i == nw) fprintf(stderr, "ERROR\n");
if(i == nw) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
kmp = kmp | (uint64_t)(aw[i].ol);
@@ -19578,7 +19578,7 @@ void merge_ug_nodes(ma_ug_t *ug, asg_t* read_g, kvec_t_u64_warp* array)
if(aw[i].del) continue;
if(aw[i].v == (v^1)) break;
}
if(i == nw) fprintf(stderr, "ERROR\n");
if(i == nw) fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
kmp = kmp | (uint64_t)(aw[i].ol);
Trio.cpp
-4
View File
@@ -20,10 +20,6 @@
#define YAK_MAGIC "YAK\2"
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#define yak_ch_eq(a, b) ((a)>>YAK_COUNTER_BITS == (b)>>YAK_COUNTER_BITS) // lower 8 bits for counts; higher bits for k-mer
#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)
KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak_ch_eq)
anchor.cpp
+34 -4
View File
@@ -17,6 +17,9 @@ KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
#define oreg_ss_lt(a, b) ((a).shared_seed > (b).shared_seed) // in the decending order
KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)
typedef struct {
int n;
const ha_idxpos_t *a;
@@ -40,7 +43,7 @@ void ha_abuf_destroy(ha_abuf_t *ab)
free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);
}
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain)
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
@@ -106,9 +109,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, band_width_threshold, keep_whole_chain);
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
calculate_overlap_region_by_chaining(cl, overlap_list, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain);
#if 0
if (overlap_list->length > 2000) {
@@ -120,4 +121,33 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
}
}
#endif
if ((int)overlap_list->length > max_n_chain) {
uint32_t n[2], s[2];
n[0] = n[1] = 0, s[0] = s[1] = 0;
for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
const overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
++n[dir];
if ((int)n[dir] == max_n_chain) s[dir] = r->shared_seed;
}
if (s[0] > 0 || s[1] > 0) {
for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->list[i];
int dir = r->x_pos_s == 0? 0 : 1;
if (r->shared_seed > s[dir]) {
if ((uint32_t)k != i) {
overlap_region t;
t = overlap_list->list[k];
overlap_list->list[k] = overlap_list->list[i];
overlap_list->list[i] = t;
}
++k;
}
}
overlap_list->length = k;
}
}
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
}
htab.h
+4
View File
@@ -81,6 +81,10 @@ static inline uint64_t yak_hash_long(uint64_t x[4])
#define MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
#define REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
#ifndef kroundup64
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, x|=(x)>>32, ++(x))
#endif