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integration/print het sites

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chhylp123
2022-01-17 18:29:48 -05:00
parent 7af0d85258
commit 0ce5a7ba5b
18 changed files with 2884 additions and 385 deletions
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194
Hash_Table.cpp
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@@ -4,6 +4,7 @@
#include <pthread.h>
#include "Hash_Table.h"
#include "ksort.h"
#include "kalloc.h"
pthread_mutex_t output_mutex;
#define overlap_region_key(a) ((a).y_id)
@@ -58,6 +59,18 @@ void destory_overlap_region_alloc(overlap_region_alloc* list)
free(list->list);
}
void destory_overlap_region_alloc_buf(void *km, overlap_region_alloc* list, int is_z)
{
uint64_t i = 0;
for (i = 0; i < list->size; i++) {
if(list->list[i].w_list_size>0) kfree(km, list->list[i].w_list);
if(list->list[i].f_cigar.size>0) kfree(km, list->list[i].f_cigar.buffer);
if(list->list[i].boundary_cigars.size>0) kfree(km, list->list[i].boundary_cigars.buffer);
}
kfree(km, list->list);
if(is_z) memset(list, 0, sizeof(*list));
}
int get_fake_gap_pos(Fake_Cigar* x, int index)
{
return (x->buffer[index]>>32);
@@ -83,15 +96,21 @@ int get_fake_gap_shift(Fake_Cigar* x, int index)
}
int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
All_reads* R_INF, int add_beg_end)
long long xLen, long long yLen, int add_beg_end, void *km)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
uint64_t sl = list->size;
list->size = list->length + 1;
kroundup64(list->size);
if(!km) {
REALLOC(list->list, list->size);
} else {
KREALLOC(km, list->list, list->size);
}
/// need to set new space to be 0
memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
memset(list->list + sl, 0, sizeof(overlap_region)*(list->size - sl));
}
if (list->length!=0 && list->list[list->length - 1].y_id==tmp->y_id)
@@ -122,36 +141,36 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
}
long long x_right_length = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
long long y_right_length = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
long long x_right_length = xLen - tmp->x_pos_e - 1;
long long y_right_length = yLen - tmp->y_pos_e - 1;
if(x_right_length <= y_right_length)
{
tmp->x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - 1;
tmp->x_pos_e = xLen - 1;
tmp->y_pos_e = tmp->y_pos_e + x_right_length;
}
else
{
tmp->x_pos_e = tmp->x_pos_e + y_right_length;
tmp->y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - 1;
tmp->y_pos_e = yLen - 1;
}
if (tmp->x_pos_strand == 1)
{
list->list[list->length].x_id = tmp->x_id;
list->list[list->length].x_pos_e = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_s - 1;
list->list[list->length].x_pos_s = Get_READ_LENGTH((*R_INF), tmp->x_id) - tmp->x_pos_e - 1;
list->list[list->length].x_pos_e = xLen - tmp->x_pos_s - 1;
list->list[list->length].x_pos_s = xLen - tmp->x_pos_e - 1;
list->list[list->length].x_pos_strand = 0;
list->list[list->length].y_id = tmp->y_id;
list->list[list->length].y_pos_e = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_s - 1;
list->list[list->length].y_pos_s = Get_READ_LENGTH((*R_INF), tmp->y_id) - tmp->y_pos_e - 1;
list->list[list->length].y_pos_e = yLen - tmp->y_pos_s - 1;
list->list[list->length].y_pos_s = yLen - tmp->y_pos_e - 1;
list->list[list->length].y_pos_strand = 1;
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
if(add_beg_end == 1)
{
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
}
long long distance_gap;
@@ -166,9 +185,8 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
if(distance_gap != pre_distance_gap)
{
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
Get_READ_LENGTH((*R_INF), tmp->x_id) - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
pre_distance_gap);
add_fake_cigar(&(list->list[list->length].f_cigar), xLen - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
pre_distance_gap, km);
}
}
@@ -178,7 +196,7 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
list->list[list->length].f_cigar.length - 1), km);
}
}
else
@@ -195,10 +213,10 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
if(add_beg_end == 1)
{
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
}
long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
@@ -218,7 +236,7 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap);
get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap, km);
}
}
@@ -228,7 +246,7 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
list->list[list->length].f_cigar.length - 1), km);
}
}
@@ -245,15 +263,20 @@ int append_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_regi
int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
ma_utg_v *ua, int add_beg_end)
ma_utg_v *ua, int add_beg_end, void *km)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
uint64_t sl = list->size;
list->size = list->length + 1;
kroundup64(list->size);
if(!km) {
REALLOC(list->list, list->size);
} else {
KREALLOC(km, list->list, list->size);
}
/// need to set new space to be 0
memset(list->list + (list->size/2), 0, sizeof(overlap_region)*(list->size/2));
memset(list->list + sl, 0, sizeof(overlap_region)*(list->size - sl));
}
if (list->length!=0 && list->list[list->length - 1].y_id==tmp->y_id)
@@ -310,10 +333,10 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
list->list[list->length].y_pos_s = ua->a[tmp->y_id].len - tmp->y_pos_e - 1;
list->list[list->length].y_pos_strand = 1;
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
if(add_beg_end == 1)
{
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
}
long long distance_gap;
@@ -330,7 +353,7 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
ua->a[tmp->x_id].len - get_fake_gap_pos(&(tmp->f_cigar), i) - 1,
pre_distance_gap);
pre_distance_gap, km);
}
}
@@ -340,7 +363,7 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
list->list[list->length].f_cigar.length - 1), km);
}
}
else
@@ -357,10 +380,10 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2));
resize_fake_cigar(&(list->list[list->length].f_cigar), (tmp->f_cigar.length + 2), km);
if(add_beg_end == 1)
{
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0);
add_fake_cigar(&(list->list[list->length].f_cigar), list->list[list->length].x_pos_s, 0, km);
}
long long distance_self_pos = tmp->x_pos_e - tmp->x_pos_s;
@@ -380,7 +403,7 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
pre_distance_gap = distance_gap;
add_fake_cigar(&(list->list[list->length].f_cigar),
get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap);
get_fake_gap_pos(&(tmp->f_cigar), i), init_distance_gap - pre_distance_gap, km);
}
}
@@ -390,7 +413,7 @@ int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_
add_fake_cigar(&(list->list[list->length].f_cigar),
list->list[list->length].x_pos_e,
get_fake_gap_shift(&(list->list[list->length].f_cigar),
list->list[list->length].f_cigar.length - 1));
list->list[list->length].f_cigar.length - 1), km);
}
}
@@ -627,7 +650,7 @@ int32_t ha_chain_check(k_mer_hit *a, int32_t n_a, Chain_Data *dp, int32_t min_sc
///double band_width_threshold = 0.05;
long long chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result,
double band_width_threshold, int max_skip, int x_readLen, int y_readLen)
double band_width_threshold, int max_skip, int x_readLen, int y_readLen, void *km)
{
long long i, j;
long long self_pos, pos, max_j, max_i, max_score, score;
@@ -640,7 +663,7 @@ long long chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region*
long long total_indels, total_self_length;
int32_t ret;
resize_Chain_Data(dp, a_n);
resize_Chain_Data(dp, a_n, km);
ret = ha_chain_check(a, a_n, dp, min_score, band_width_threshold);
if (ret > 0) {
@@ -771,7 +794,7 @@ skip_dp:
///record first site
///the length of f_cigar should be at least 1
///record the offset of reference
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap, km);
long long chainLen = 0;
if(result->x_pos_strand == 1)
{
@@ -784,7 +807,7 @@ skip_dp:
{
pre_distance_gap = distance_gap;
///record this site
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap, km);
}
chainLen++;
@@ -803,12 +826,12 @@ skip_dp:
if(distance_gap == pre_distance_gap)
{
result->f_cigar.length--;
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap, km);
}
else
{
pre_distance_gap = distance_gap;
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap);
add_fake_cigar(&(result->f_cigar), a[i].self_offset, pre_distance_gap, km);
}
chainLen++;
@@ -823,16 +846,13 @@ skip_dp:
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end, overlap_region* f_cigar)
uint64_t readID, uint64_t readLength, All_reads* R_INF, const ul_idx_t *uref, double band_width_threshold, int add_beg_end, overlap_region* f_cigar, void *km)
{
long long i = 0;
uint64_t current_ID;
uint64_t current_stand;
if (candidates->length == 0)
{
return;
}
if (candidates->length == 0) return;
long long sub_region_beg;
long long sub_region_end;
@@ -875,32 +895,34 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
chain_DP(candidates->list + sub_region_beg,
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), f_cigar, band_width_threshold,
25, Get_READ_LENGTH((*R_INF), (*f_cigar).x_id), Get_READ_LENGTH((*R_INF), (*f_cigar).y_id));
25, /**Get_READ_LENGTH((*R_INF), (*f_cigar).x_id)**/readLength,
R_INF?Get_READ_LENGTH((*R_INF), (*f_cigar).y_id):uref->ug->u.a[(*f_cigar).y_id].len, km);
///if (tmp_region.x_id != tmp_region.y_id && tmp_region.shared_seed > 1)
if ((*f_cigar).x_id != (*f_cigar).y_id)
{
append_inexact_overlap_region_alloc(overlap_list, f_cigar, R_INF, add_beg_end);
append_inexact_overlap_region_alloc(overlap_list, f_cigar, readLength, R_INF?Get_READ_LENGTH((*R_INF), (*f_cigar).y_id):uref->ug->u.a[(*f_cigar).y_id].len, add_beg_end, km);
}
}
}
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end, int error_threshold)
int extra_begin, int extra_end, int error_threshold, int blockLen, void *km)
{
long long length = region->x_pos_e - region->x_pos_s + 1;
///the length of window may large or small than WINDOW
/****************************may have bugs********************************/
uint64_t num_windows = length / WINDOW + 4;
uint64_t num_windows = length / blockLen + 4;
/****************************may have bugs********************************/
///w_list_length has alredy set to be 0 at clear_overlap_region_alloc
if (num_windows > region->w_list_size)
{
region->w_list_size = num_windows;
region->w_list = (window_list*)realloc(region->w_list, region->w_list_size*sizeof(window_list));
if(!km) REALLOC(region->w_list, region->w_list_size);
else KREALLOC(km, region->w_list, region->w_list_size);
}
@@ -967,17 +989,26 @@ void destory_Chain_Data(Chain_Data* x)
free(x->tmp);
}
void resize_Chain_Data(Chain_Data* x, long long size)
void resize_Chain_Data(Chain_Data* x, long long size, void *km)
{
if (size + 1 > x->size) {
x->size = size + 1;
kroundup64(x->size);
REALLOC(x->score, x->size);
REALLOC(x->pre, x->size);
REALLOC(x->indels, x->size);
REALLOC(x->self_length, x->size);
REALLOC(x->occ, x->size);
REALLOC(x->tmp, x->size);
if(!km) {
REALLOC(x->score, x->size);
REALLOC(x->pre, x->size);
REALLOC(x->indels, x->size);
REALLOC(x->self_length, x->size);
REALLOC(x->occ, x->size);
REALLOC(x->tmp, x->size);
} else {
KREALLOC(km, x->score, x->size);
KREALLOC(km, x->pre, x->size);
KREALLOC(km, x->indels, x->size);
KREALLOC(km, x->self_length, x->size);
KREALLOC(km, x->occ, x->size);
KREALLOC(km, x->tmp, x->size);
}
}
}
@@ -1001,6 +1032,18 @@ void destory_Candidates_list(Candidates_list* l)
destory_Chain_Data(&(l->chainDP));
}
void destory_Candidates_list_buf(void *km, Candidates_list* l, int is_z)
{
kfree(km, l->list);
kfree(km, l->chainDP.score);
kfree(km, l->chainDP.pre);
kfree(km, l->chainDP.indels);
kfree(km, l->chainDP.self_length);
kfree(km, l->chainDP.occ);
kfree(km, l->chainDP.tmp);
if(is_z) memset(l, 0, sizeof(*l));
}
void init_fake_cigar(Fake_Cigar* x)
{
x->buffer = NULL;
@@ -1021,12 +1064,18 @@ void clear_fake_cigar(Fake_Cigar* x)
x->length = 0;
}
void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift)
void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift, void *km)
{
if(x->length + 1 > x->size)
{
x->size = (x->length + 1) * 2;
x->buffer = (uint64_t*)realloc(x->buffer, sizeof(uint64_t) * x->size);
x->size = x->length + 1;
kroundup32(x->size);
if(!km) {
REALLOC(x->buffer, x->size);
} else {
KREALLOC(km, x->buffer, x->size);
}
// x->buffer = (uint64_t*)realloc(x->buffer, sizeof(uint64_t) * x->size);
}
x->buffer[x->length] = gap_site;
@@ -1051,11 +1100,17 @@ 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)
void resize_fake_cigar(Fake_Cigar* x, uint64_t size, void *km)
{
if (size > x->size) {
x->size = size;
REALLOC(x->buffer, x->size);
if(!km) {
REALLOC(x->buffer, x->size);
}
else {
KREALLOC(km, x->buffer, x->size);
}
}
x->length = 0;
}
@@ -1081,18 +1136,15 @@ void destory_window_list_alloc(window_list_alloc* x)
}
}
void resize_window_list_alloc(window_list_alloc* x, long long size)
void resize_window_list_alloc(window_list_alloc* x, long long size, void *km)
{
if(size > x->size)
{
if(size > x->size){
x->size = size;
x->buffer = (window_list*)realloc(x->buffer, sizeof(window_list) * x->size);
if(!km) REALLOC(x->buffer, x->size);
else KREALLOC(km, x->buffer, x->size);
}
long long i;
for (i = 0; i < x->size; i++)
{
x->buffer[i].error = -1;
}
for (i = 0; i < x->size; i++) x->buffer[i].error = -1;
x->length = 0;
}