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graphPath.c
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/*
The MIT License (MIT)
Copyright (c) 2024 Hanfc <h2624366594@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include <stdio.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <stdbool.h>
#include <pthread.h>
#include "khash.h"
#include "BFSseed.h"
#include "hitseeds.h"
#include "graphtools.h"
#include "misc.h"
#include "log.h"
typedef struct {
int* node;
int* utr;
int type;
uint32_t nodenum;
uint64_t nodelen;
uint64_t pathlen;
} nodePath;
typedef struct {
int node;
int utr;
} NodeUtrPair;
typedef struct {
int* node3;
int* node3utr;
int* node5;
int* node5utr;
int node3num;
int node5num;
} nodeLink;
KHASH_MAP_INIT_INT(node_num, int)
KHASH_MAP_INIT_INT(Ha_nodelink, nodeLink)
KHASH_MAP_INIT_INT(Ha_nodedepth, int)
static khash_t(Ha_nodedepth) *g_sort_hash = NULL;
pthread_mutex_t mutex;
uint32_t max_node = 1;
uint32_t mt_uniq = 0;
uint64_t mt_uniq_len = 0;
uint8_t taxo_index = 0;
typedef struct {
int* path;
int* utr;
khash_t(node_num) *h_mito;
khash_t(node_num) *h_chloro;
int type;
uint32_t nodenum;
uint64_t pathlen;
} mpath;
typedef struct {
int node1;
int utr1;
int node2;
int utr2;
int main_num;
BFSlinks* mainlinks;
CtgDepth* ctg_depth;
nodePath* current_path;
pathScore* path_score;
int* mt_contigs;
int mt_num;
khash_t(node_num) *h_mito;
int* pt_contigs;
int pt_num;
khash_t(node_num) *h_chloro;
khash_t(Ha_nodelink) *h_links;
int stop_flag;
} bfs_m_args;
void copy_BFSlinks(BFSlinks* dest, const BFSlinks* src) {
dest->lctgsmp = src->lctgsmp;
dest->lctgdepth = src->lctgdepth;
dest->lctglen = src->lctglen;
dest->rctgsmp = src->rctgsmp;
dest->rctgdepth = src->rctgdepth;
dest->rctglen = src->rctglen;
dest->linkdepth = src->linkdepth;
dest->lutrsmp = src->lutrsmp;
dest->rutrsmp = src->rutrsmp;
// dest->lctg = src->lctg ? strdup(src->lctg) : NULL;
// dest->rctg = src->rctg ? strdup(src->rctg) : NULL;
// dest->lutr = src->lutr ? strdup(src->lutr) : NULL;
// dest->rutr = src->rutr ? strdup(src->rutr) : NULL;
}
// void free_BFSlinks(BFSlinks *links, int num_links) {
// for (int i = 0; i < num_links; i++) {
// if (links[i].lctg) free(links[i].lctg);
// if (links[i].rctg) free(links[i].rctg);
// if (links[i].lutr) free(links[i].lutr);
// if (links[i].rutr) free(links[i].rutr);
// }
// free(links);
// }
static void node_recursive(int node, bool* link_used, int* visited_nodes, int* visited_num, int link_num, BFSlinks* links, BFSlinks* tempBFSlinks, int* temp_link_num, int* temp_node, int* temp_node_num) {
visited_nodes[*visited_num] = node;
(*visited_num)++;
uint64_t i;
for (i = 0; i < link_num; i++) {
if (link_used[i]) continue;
if (links[i].lctgsmp == node) {
copy_BFSlinks(&tempBFSlinks[*temp_link_num], &links[i]);
(*temp_link_num)++;
link_used[i] = true;
if (findint(temp_node, *temp_node_num, links[i].rctgsmp) == 0) {
temp_node[*temp_node_num] = links[i].rctgsmp;
(*temp_node_num)++;
}
node_recursive(links[i].rctgsmp, link_used, visited_nodes, visited_num, link_num, links, tempBFSlinks, temp_link_num, temp_node, temp_node_num);
} else if (links[i].rctgsmp == node) {
copy_BFSlinks(&tempBFSlinks[*temp_link_num], &links[i]);
(*temp_link_num)++;
link_used[i] = true;
if (findint(temp_node, *temp_node_num, links[i].lctgsmp) == 0) {
temp_node[*temp_node_num] = links[i].lctgsmp;
(*temp_node_num)++;
}
node_recursive(links[i].lctgsmp, link_used, visited_nodes, visited_num, link_num, links, tempBFSlinks, temp_link_num, temp_node, temp_node_num);
}
}
}
uint32_t bfs_structure(int node_num, int link_num, BFSlinks* links, int* node_arry, khash_t(Ha_structures)* h_structures) {
int* visited_nodes = (int*)malloc(2 * (link_num + 1) * sizeof(int));
bool* link_used = (bool*)malloc((link_num + 1) * sizeof(bool));
memset(link_used, 0, link_num * sizeof(bool));
int visited_num = 0;
uint32_t structure_num = 0;
int ret;
khint_t k;
uint64_t i, j;
for (i = 0; i < node_num; i++) {
int node = node_arry[i];
if (findint(visited_nodes, visited_num, node) == 0) {
BFSlinks* tempBFSlinks = (BFSlinks*)malloc((link_num + 1) * sizeof(BFSlinks));
int temp_link_num = 0;
int* temp_node = (int*)malloc(node_num * sizeof(int));
int temp_node_num = 1;
temp_node[0] = node;
k = kh_put(Ha_structures, h_structures, structure_num, &ret);
structure_num++;
if (ret) {
node_recursive(node, link_used, visited_nodes, &visited_num, link_num, links, tempBFSlinks, &temp_link_num, temp_node, &temp_node_num);
BFSstructure *structure = (BFSstructure*)malloc(sizeof(BFSstructure));
structure->num_links = temp_link_num;
structure->links = (BFSlinks*)malloc((temp_link_num + 1) * sizeof(BFSlinks));
for (j = 0; j < temp_link_num; j++) {
copy_BFSlinks(&structure->links[j], &tempBFSlinks[j]);
}
structure->num_nodes = temp_node_num;
structure->node = (int*)malloc(temp_node_num * sizeof(int));
for (j = 0; j < temp_node_num; j++) {
structure->node[j] = temp_node[j];
}
kh_value(h_structures, k) = structure;
}
free(tempBFSlinks);
}
}
free(visited_nodes);
free(link_used);
return structure_num;
}
static void bfs_algorithm(int node_s, int s_utr, int node_t, int t_utr, int main_num, BFSlinks* mainlinks, CtgDepth *ctg_depth, nodePath* current_path, nodePath** all_paths, int* path_count)
{
/* check if the current node is the target node */
if (node_s == node_t && s_utr != t_utr) {
*all_paths = (nodePath*)realloc(*all_paths, (*path_count + 1) * sizeof(nodePath));
(*all_paths)[*path_count] = *current_path;
(*all_paths)[*path_count].pathlen = current_path->nodelen;
(*all_paths)[*path_count].type = 0;
(*path_count)++;
return;
}
/* find all paths from node_s to node_t */
uint64_t i;
for (i = 0; i < main_num; i++) {
if (mainlinks[i].lctgsmp == node_s && s_utr != mainlinks[i].lutrsmp) {
current_path->nodenum++;
current_path->node = (int*)realloc(current_path->node, current_path->nodenum * sizeof(int));
current_path->node[current_path->nodenum - 1] = mainlinks[i].rctgsmp;
current_path->utr = (int*)realloc(current_path->utr, current_path->nodenum * sizeof(int));
current_path->utr[current_path->nodenum - 1] = mainlinks[i].rutrsmp;
current_path->nodelen += ctg_depth[mainlinks[i].rctgsmp - 1].len;
bfs_algorithm(mainlinks[i].rctgsmp, mainlinks[i].rutrsmp, node_t, t_utr, main_num, mainlinks, ctg_depth, current_path, all_paths, path_count);
/* backtrack */
current_path->nodenum--;
current_path->nodelen -= ctg_depth[mainlinks[i].rctgsmp - 1].len;
}
else if (mainlinks[i].rctgsmp == node_s && s_utr != mainlinks[i].rutrsmp) {
current_path->nodenum++;
current_path->node = (int*)realloc(current_path->node, current_path->nodenum * sizeof(int));
current_path->node[current_path->nodenum - 1] = mainlinks[i].lctgsmp;
current_path->utr = (int*)realloc(current_path->utr, current_path->nodenum * sizeof(int));
current_path->utr[current_path->nodenum - 1] = mainlinks[i].lutrsmp;
current_path->nodelen += ctg_depth[mainlinks[i].lctgsmp - 1].len;
bfs_algorithm(mainlinks[i].lctgsmp, mainlinks[i].lutrsmp, node_t, t_utr, main_num, mainlinks, ctg_depth, current_path, all_paths, path_count);
/* backtrack */
current_path->nodenum--;
current_path->nodelen -= ctg_depth[mainlinks[i].lctgsmp - 1].len;
}
}
}
void findSpath(int node1, int node1utr, int node2, int node2utr, int main_num, BFSlinks* mainlinks, CtgDepth *ctg_depth)
{
nodePath* all_paths = NULL;
int path_count = 0;
nodePath current_path;
current_path.nodenum = 1;
current_path.node = (int*)malloc(current_path.nodenum * sizeof(int));
current_path.node[0] = node1;
current_path.utr = (int*)malloc(current_path.nodenum * sizeof(int));
current_path.utr[0] = node1utr;
current_path.nodelen = ctg_depth[node1 - 1].len;
current_path.pathlen = 0;
bfs_algorithm(node1, node1utr, node2, node2utr, main_num, mainlinks, ctg_depth, ¤t_path, &all_paths, &path_count);
nodePath* shortest_path = &all_paths[0];
uint64_t i;
for (i = 1; i < path_count; i++) {
if (all_paths[i].pathlen < shortest_path->pathlen) {
shortest_path = &all_paths[i];
}
}
if (shortest_path->nodenum > 1) {
log_info("-- %d", shortest_path->pathlen);
for (i = 0; i < shortest_path->nodenum; i++) {
log_info("%d %d -> ", shortest_path->node[i], shortest_path->utr[i]);
}
log_info("\n");
}
for (i = 0; i < path_count; i++) {
free(all_paths[i].node);
free(all_paths[i].utr);
}
free(all_paths);
free(current_path.node);
free(current_path.utr);
}
static int path_up(pathScore* path_score, nodePath current_path, CtgDepth *ctg_depth, int mt_ctg, int* mt_ctgarr, int pt_ctg, int* pt_ctgarr)
{
int mt_num = 0;
int uniq_mtnum = 0;
uint64_t uniq_mtlen = 0;
uint64_t uniq_ptlen = 0;
int pt_num = 0;
int uniq_ptnum = 0;
uint32_t node_num = current_path.nodenum;
uint64_t path_len = current_path.nodelen;
int* pathutr = current_path.utr;
int* path_node = current_path.node;
int type = current_path.type;
int* temp_mtarr = (int*)malloc(current_path.nodenum * sizeof(int));
int* temp_ptarr = (int*)malloc(current_path.nodenum * sizeof(int));
uint64_t i;
for (i = 0; i < current_path.nodenum; i++)
{
if (findint(pt_ctgarr, pt_ctg, path_node[i]) == 1 && findint(temp_ptarr, uniq_ptnum, path_node[i]) == 0) {
temp_ptarr[uniq_ptnum] = path_node[i];
uniq_ptlen += ctg_depth[path_node[i] - 1].len;
uniq_ptnum++;
pt_num++;
} else if (findint(pt_ctgarr, pt_ctg, path_node[i]) == 1 && findint(temp_ptarr, uniq_ptnum, path_node[i]) == 1) {
pt_num++;
} else if (findint(mt_ctgarr, mt_ctg, path_node[i]) == 1 && findint(temp_mtarr, uniq_mtnum, path_node[i]) == 0) {
temp_mtarr[uniq_mtnum] = path_node[i];
uniq_mtlen += ctg_depth[path_node[i] - 1].len;
uniq_mtnum++;
mt_num++;
} else if (findint(mt_ctgarr, mt_ctg, path_node[i]) == 1 && findint(temp_mtarr, uniq_mtnum, path_node[i]) == 1) {
mt_num++;
}
}
free(temp_mtarr);
free(temp_ptarr);
pthread_mutex_lock(&mutex);
path_score->inval_num++;
int update_flag = 0;
if (taxo_index == 1) {
if (uniq_mtlen > path_score->uniq_mt_pathlen) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum > path_score->uniq_mt_nodenum) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type < path_score->type) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && mt_num > path_score->mt_nodenum) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && mt_num == path_score->mt_nodenum && path_len < path_score->path_len) {
update_flag = 1;
}
} else {
if (uniq_mtlen > path_score->uniq_mt_pathlen) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum > path_score->uniq_mt_nodenum) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type < path_score->type) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && mt_num > path_score->mt_nodenum) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && mt_num == path_score->mt_nodenum && path_len < path_score->path_len) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && path_len == path_score->path_len && mt_num == path_score->mt_nodenum && uniq_ptnum < path_score->uniq_pt_nodenum) {
update_flag = 1;
} else if (uniq_mtlen == path_score->uniq_mt_pathlen && uniq_mtnum == path_score->uniq_mt_nodenum && type == path_score->type && path_len == path_score->path_len && mt_num == path_score->mt_nodenum && uniq_ptnum == path_score->uniq_pt_nodenum && pt_num < path_score->pt_nodenum) {
update_flag = 1;
}
}
if (update_flag) {
path_score->inval_num = 0;
path_score->uniq_mt_pathlen = uniq_mtlen;
path_score->uniq_mt_nodenum = uniq_mtnum;
path_score->mt_nodenum = mt_num;
path_score->pt_nodenum = pt_num;
path_score->uniq_pt_nodenum = uniq_ptnum;
path_score->node_num = node_num;
float rato = (float)path_score->uniq_mt_pathlen / mt_uniq_len;
path_score->path_len = path_len;
path_score->type = type;
// printf("The length of pt %ld\n", uniq_ptlen);
// printf("Graph path %s %.2f%% %ld bp:\n-- ", path_score->type == 0 ? "C" : "L", rato * 100, path_score->path_len);
// printf("Path upate: ");
for (i = 0; i < node_num; i++) {
path_score->path_node[i] = path_node[i];
path_score->path_utr[i] = pathutr[i];
// printf("%d %d -> ", path_node[i], pathutr[i]);
}
// printf("\n");
}
pthread_mutex_unlock(&mutex);
if (path_score->inval_num > 10000000) {
return 1;
}
return 0;
}
static void bfs_m(int node_s, int s_utr, int node_t, int t_utr, int main_num, BFSlinks* mainlinks, CtgDepth *ctg_depth, nodePath* current_path, pathScore* path_score,
int* mt_contigs, int mt_num, khash_t(node_num) *h_mito, int* pt_contigs, int pt_num, khash_t(node_num) *h_chloro, khash_t(Ha_nodelink) *h_links, int* stop_flag)
{
if (*stop_flag) return;
/* check if the current node is the target node */
if (current_path->nodenum > 1 && node_s == node_t && s_utr != t_utr) {
current_path->type = 0;
current_path->nodelen -= ctg_depth[node_t - 1].len;
*stop_flag = path_up(path_score, *current_path, ctg_depth, mt_num, mt_contigs, pt_num, pt_contigs);
current_path->nodelen += ctg_depth[node_t - 1].len;
return;
}
int* temp_mtarr = (int*)malloc(current_path->nodenum * sizeof(int));
int uniq_mtnum = 0;
uint64_t uniq_mtlen = 0;
uint64_t i;
for (i = 0; i < current_path->nodenum; i++)
{
if (findint(mt_contigs, mt_num, current_path->node[i]) == 1
&& findint(temp_mtarr, uniq_mtnum, current_path->node[i]) == 0
&& findint(pt_contigs, pt_num, current_path->node[i]) == 0) {
temp_mtarr[uniq_mtnum] = current_path->node[i];
uniq_mtlen += ctg_depth[current_path->node[i] - 1].len;
uniq_mtnum++;
}
}
free(temp_mtarr);
float rato = (float)uniq_mtlen / mt_uniq_len;
if (rato > 0.5) {
*stop_flag = path_up(path_score, *current_path, ctg_depth, mt_num, mt_contigs, pt_num, pt_contigs);
}
/* find all paths from node_s to node_t */
khint_t is_node_s = kh_get(Ha_nodelink, h_links, node_s);
if (is_node_s == kh_end(h_links)) return;
nodeLink* link_s = &kh_value(h_links, is_node_s);
/* Direction checking logic */
int* node_array = s_utr == 3 ? link_s->node5 : link_s->node3;
int* utr_array = s_utr == 3 ? link_s->node5utr : link_s->node3utr;
int node_num = s_utr == 3 ? link_s->node5num : link_s->node3num;
bool path_stop = true;
for (i = 0; i < node_num; i++)
{
int next_node = node_array[i];
int next_utr = utr_array[i];
bool is_chloro = kh_get(node_num, h_chloro, next_node) != kh_end(h_chloro);
bool is_mito = kh_get(node_num, h_mito, next_node) != kh_end(h_mito);
if (is_chloro && kh_value(h_chloro, kh_get(node_num, h_chloro, next_node)) > 0) continue;
if (is_mito && kh_value(h_mito, kh_get(node_num, h_mito, next_node)) == 0) continue;
/* Add node to path */
current_path->node[current_path->nodenum] = next_node;
current_path->utr[current_path->nodenum] = next_utr;
current_path->nodelen += ctg_depth[next_node - 1].len;
current_path->nodenum++;
if (is_mito) kh_value(h_mito, kh_get(node_num, h_mito, next_node))--;
if (is_chloro) kh_value(h_chloro, kh_get(node_num, h_chloro, next_node))++;
path_stop = false;
/* Recursively call bfs_m */
bfs_m(next_node, next_utr, node_t, t_utr, main_num, mainlinks, ctg_depth, current_path, path_score, mt_contigs, mt_num, h_mito, pt_contigs, pt_num, h_chloro, h_links, stop_flag);
/* Backtrack */
current_path->type = 1;
current_path->nodenum--;
current_path->nodelen -= ctg_depth[next_node - 1].len;
if (is_mito) kh_value(h_mito, kh_get(node_num, h_mito, next_node))++;
if (is_chloro) kh_value(h_chloro, kh_get(node_num, h_chloro, next_node))--;
}
current_path->type = 1;
/* End if no path is found */
if (path_stop) *stop_flag = path_up(path_score, *current_path, ctg_depth, mt_num, mt_contigs, pt_num, pt_contigs);
}
static int compare_by_hash_value(const void* a, const void* b) {
const NodeUtrPair* pair_a = (const NodeUtrPair*)a;
const NodeUtrPair* pair_b = (const NodeUtrPair*)b;
int key_a = pair_a->node;
int key_b = pair_b->node;
khint_t ka = kh_get(Ha_nodedepth, g_sort_hash, key_a);
khint_t kb = kh_get(Ha_nodedepth, g_sort_hash, key_b);
if (ka == kh_end(g_sort_hash) || kb == kh_end(g_sort_hash)) {
return 0;
}
int value_a = kh_value(g_sort_hash, ka);
int value_b = kh_value(g_sort_hash, kb);
return value_b - value_a;
}
int kh_copy(khash_t(node_num) *dst, khash_t(node_num) *src) {
khiter_t k;
int ret;
for (k = kh_begin(src); k != kh_end(src); ++k) {
if (kh_exist(src, k)) {
int key = kh_key(src, k);
int value = kh_val(src, k);
khiter_t d = kh_put(node_num, dst, key, &ret);
if (ret != -1) {
kh_val(dst, d) = value;
}
}
}
return 0;
}
void bfsMap(int nodes, int utrs, int nodet, int utrt, CtgDepth *ctg_depth, mpath* current_path, khash_t(Ha_nodelink) *h_links, int max_paths, khash_t(node_num) *h_mito, khash_t(node_num) *h_chloro, int* path_t)
{
typedef struct {
mpath mpath[2*max_paths];
int flag[2*max_paths];
int path_count;
} bfsPath;
bfsPath bfs_path;
bfs_path.path_count = 1;
bfs_path.mpath[0].nodenum = 1;
bfs_path.mpath[0].path = (int*)malloc(max_node * sizeof(int));
bfs_path.mpath[0].utr = (int*)malloc(max_node * sizeof(int));
bfs_path.mpath[0].type = 1;
bfs_path.mpath[0].pathlen = ctg_depth[nodes - 1].len;
bfs_path.mpath[0].path[0] = nodes;
bfs_path.mpath[0].utr[0] = utrs;
bfs_path.mpath[0].h_mito = kh_init(node_num);
bfs_path.mpath[0].h_chloro = kh_init(node_num);
kh_copy(bfs_path.mpath[0].h_mito, h_mito);
kh_copy(bfs_path.mpath[0].h_chloro, h_chloro);
uint64_t i, j;
for (i = 0; i < 2*max_paths; i++) {
bfs_path.flag[i] = 1;
}
int dy_path_count = 1;
int dy_temp_end = 0;
while (1)
{
int temp_end = 0;
for (i = 0; i < dy_path_count; i++)
{
if (bfs_path.flag[i] == 0) continue;
temp_end = 1;
int endutr = bfs_path.mpath[i].utr[bfs_path.mpath[i].nodenum - 1];
int endnode = bfs_path.mpath[i].path[bfs_path.mpath[i].nodenum - 1];
khiter_t k = kh_get(Ha_nodelink, h_links, endnode);
if (k == kh_end(h_links)) {
continue;
}
nodeLink* node_links = &kh_val(h_links, k);
int* tempmap = endutr == 3 ? node_links->node5 : node_links->node3;
int* temputr = endutr == 3 ? node_links->node5utr : node_links->node3utr;
int tempmapnum = endutr == 3 ? node_links->node5num : node_links->node3num;
if (tempmapnum == 1 && bfs_path.flag[i] == 1) {
if (tempmap[0] == nodet && temputr[0] == utrt) {
bfs_path.flag[i] = 0;
continue;
}
bool is_chloro = kh_get(node_num, bfs_path.mpath[i].h_chloro, tempmap[0]) != kh_end(bfs_path.mpath[i].h_chloro);
bool is_mito = kh_get(node_num, bfs_path.mpath[i].h_mito, tempmap[0]) != kh_end(bfs_path.mpath[i].h_mito);
if (is_chloro && kh_value(bfs_path.mpath[i].h_chloro, kh_get(node_num, bfs_path.mpath[i].h_chloro, tempmap[0])) > 1) {bfs_path.flag[i] = 0; continue;}
if (is_mito && kh_value(bfs_path.mpath[i].h_mito, kh_get(node_num, bfs_path.mpath[i].h_mito, tempmap[0])) == 0) {bfs_path.flag[i] = 0; continue;}
if (is_mito) kh_value(bfs_path.mpath[i].h_mito, kh_get(node_num, bfs_path.mpath[i].h_mito, tempmap[0]))--;
if (is_chloro) kh_value(bfs_path.mpath[i].h_chloro, kh_get(node_num, bfs_path.mpath[i].h_chloro, tempmap[0]))++;
bfs_path.mpath[i].nodenum++;
bfs_path.mpath[i].path = (int*)realloc(bfs_path.mpath[i].path, bfs_path.mpath[i].nodenum * sizeof(int));
bfs_path.mpath[i].utr = (int*)realloc(bfs_path.mpath[i].utr, bfs_path.mpath[i].nodenum * sizeof(int));
bfs_path.mpath[i].path[bfs_path.mpath[i].nodenum - 1] = tempmap[0];
bfs_path.mpath[i].pathlen += ctg_depth[tempmap[0] - 1].len;
bfs_path.mpath[i].utr[bfs_path.mpath[i].nodenum - 1] = temputr[0];
if (tempmap[0] == nodet) {
bfs_path.flag[i] = 0;
bfs_path.mpath[i].type = 0;
continue;
}
bfs_path.mpath[i].type = 1;
} else if (tempmapnum > 1 && bfs_path.flag[i] == 1) {
mpath temp_mpath = bfs_path.mpath[i];
int dy_path_index = i;
for (j = 0; j < tempmapnum; j++)
{
if (tempmap[0] == nodet && temputr[0] == utrt) {
bfs_path.flag[i] = 0;
break;
}
bool is_chloro = kh_get(node_num, bfs_path.mpath[i].h_chloro, tempmap[j]) != kh_end(bfs_path.mpath[i].h_chloro);
bool is_mito = kh_get(node_num, bfs_path.mpath[i].h_mito, tempmap[j]) != kh_end(bfs_path.mpath[i].h_mito);
if (is_chloro && kh_value(bfs_path.mpath[i].h_chloro, kh_get(node_num, bfs_path.mpath[i].h_chloro, tempmap[j])) > 1) {bfs_path.flag[dy_path_index] = 0; continue;}
if (is_mito && kh_value(bfs_path.mpath[i].h_mito, kh_get(node_num, bfs_path.mpath[i].h_mito, tempmap[j])) == 0) {bfs_path.flag[dy_path_index] = 0; continue;}
bfs_path.mpath[dy_path_index].nodenum = temp_mpath.nodenum;
bfs_path.mpath[dy_path_index].path = (int*)malloc(max_node * sizeof(int));
memcpy(bfs_path.mpath[dy_path_index].path, temp_mpath.path, temp_mpath.nodenum * sizeof(int));
bfs_path.mpath[dy_path_index].utr = (int*)malloc(max_node * sizeof(int));
memcpy(bfs_path.mpath[dy_path_index].utr, temp_mpath.utr, temp_mpath.nodenum * sizeof(int));
bfs_path.mpath[dy_path_index].pathlen = temp_mpath.pathlen;
bfs_path.mpath[dy_path_index].type = 1;
bfs_path.mpath[dy_path_index].h_mito = kh_init(node_num);
bfs_path.mpath[dy_path_index].h_chloro = kh_init(node_num);
kh_copy(bfs_path.mpath[dy_path_index].h_mito, temp_mpath.h_mito);
kh_copy(bfs_path.mpath[dy_path_index].h_chloro, temp_mpath.h_chloro);
if (is_mito) kh_value(bfs_path.mpath[dy_path_index].h_mito, kh_get(node_num, bfs_path.mpath[dy_path_index].h_mito, tempmap[j]))--;
if (is_chloro) kh_value(bfs_path.mpath[dy_path_index].h_chloro, kh_get(node_num, bfs_path.mpath[dy_path_index].h_chloro, tempmap[j]))++;
bfs_path.mpath[dy_path_index].nodenum++;
bfs_path.mpath[dy_path_index].path[bfs_path.mpath[dy_path_index].nodenum - 1] = tempmap[j];
bfs_path.mpath[dy_path_index].utr[bfs_path.mpath[dy_path_index].nodenum - 1] = temputr[j];
bfs_path.mpath[dy_path_index].pathlen += ctg_depth[tempmap[j] - 1].len;
if (tempmap[j] == nodet) {
bfs_path.flag[dy_path_index] = 0;
bfs_path.mpath[dy_path_index].type = 0;
}
dy_path_index = bfs_path.path_count;
bfs_path.path_count++;
}
bfs_path.path_count--;
} else if (tempmapnum == 0 && bfs_path.flag[i] == 1) {
bfs_path.flag[i] = 0;
}
}
if (bfs_path.path_count >= max_paths || temp_end == 0) {
break;
}
dy_path_count = bfs_path.path_count;
}
*path_t = 0;
for (i = 0; i < bfs_path.path_count; i++) {
// int sk = 0;
// for (int j = 0; j < bfs_path.mpath[i].nodenum; j++)
// {
// bool is_chloro = kh_get(node_num, bfs_path.mpath[i].h_chloro, bfs_path.mpath[i].path[j]) != kh_end(bfs_path.mpath[i].h_chloro);
// bool is_mito = kh_get(node_num, bfs_path.mpath[i].h_mito, bfs_path.mpath[i].path[j]) != kh_end(bfs_path.mpath[i].h_mito);
// if (is_chloro && kh_value(bfs_path.mpath[i].h_chloro, kh_get(node_num, bfs_path.mpath[i].h_chloro, bfs_path.mpath[i].path[j])) > 1) {
// sk = 1;
// break;
// }
// if (is_mito && (kh_value(bfs_path.mpath[i].h_mito, kh_get(node_num, bfs_path.mpath[i].h_mito, bfs_path.mpath[i].path[j])) < 0)) {
// sk = 1;
// break;
// }
// }
// if (sk == 1) continue;
current_path[*path_t].nodenum = bfs_path.mpath[i].nodenum;
current_path[*path_t].pathlen = bfs_path.mpath[i].pathlen;
current_path[*path_t].type = bfs_path.mpath[i].type;
current_path[*path_t].path = (int*)malloc(max_node * sizeof(int));
current_path[*path_t].utr = (int*)malloc(max_node * sizeof(int));
memcpy(current_path[*path_t].path, bfs_path.mpath[i].path, bfs_path.mpath[i].nodenum * sizeof(int));
memcpy(current_path[*path_t].utr, bfs_path.mpath[i].utr, bfs_path.mpath[i].nodenum * sizeof(int));
current_path[*path_t].h_mito = kh_init(node_num);
current_path[*path_t].h_chloro = kh_init(node_num);
kh_copy(current_path[*path_t].h_mito, bfs_path.mpath[i].h_mito);
kh_copy(current_path[*path_t].h_chloro, bfs_path.mpath[i].h_chloro);
(*path_t)++;
}
for (i = 0; i < bfs_path.path_count; i++) {
free(bfs_path.mpath[i].path);
free(bfs_path.mpath[i].utr);
kh_destroy(node_num, bfs_path.mpath[i].h_mito);
kh_destroy(node_num, bfs_path.mpath[i].h_chloro);
}
}
void* thread_bfs_m(void* args) {
bfs_m_args* bfs_args = (bfs_m_args*)args;
bfs_m(bfs_args->node1, bfs_args->utr1, bfs_args->node2, bfs_args->utr2,
bfs_args->main_num, bfs_args->mainlinks, bfs_args->ctg_depth,
bfs_args->current_path, bfs_args->path_score,
bfs_args->mt_contigs, bfs_args->mt_num, bfs_args->h_mito,
bfs_args->pt_contigs, bfs_args->pt_num, bfs_args->h_chloro,
bfs_args->h_links, &bfs_args->stop_flag);
return NULL;
}
void findMpath(int node1, int node1utr, int node2, int node2utr, int main_num, BFSlinks* mainlinks, CtgDepth *ctg_depth,
int* mt_contigs, int mt_num, int* pt_contigs, int pt_num, int* flag_err, float* mt_ratio, int taxo, pathScore* struc_path)
{
taxo_index = taxo;
max_node = 1;
mt_uniq = 0;
mt_uniq_len = 0;
int mt_depth = ctg_depth[node1 - 1].depth;
float min_depth = mt_depth;
uint64_t i, j;
for (i = 0; i < mt_num; i++)
{
if (findint(pt_contigs, pt_num, mt_contigs[i]) == 0) {
if (ctg_depth[mt_contigs[i] - 1].depth < min_depth && ctg_depth[mt_contigs[i] - 1].len > 1000 && ctg_depth[mt_contigs[i] - 1].depth > 0.5*mt_depth) {
min_depth = ctg_depth[mt_contigs[i] - 1].depth;
}
}
}
int ret;
khint_t k;
/* Initialize hash tables for mitochondria and chloroplast contigs */
khash_t(node_num) *h_mito = kh_init(node_num);
khash_t(node_num) *h_chloro = kh_init(node_num);
khash_t(Ha_nodelink) *h_links = kh_init(Ha_nodelink);
khash_t(Ha_nodedepth) *h_depth = kh_init(Ha_nodedepth);
/* Calculate max pass count for mitochondria contigs */
int maxnum_mito = 0;
// for (int i = 0; i < mt_num; i++)
// {
// if (findint(pt_contigs, pt_num, mt_contigs[i]) == 0) {
// k = kh_put(node_num, h_mito, mt_contigs[i], &ret);
// kh_value(h_mito, k) = (int)(ctg_depth[mt_contigs[i] - 1].depth / ((mt_depth + min_depth) / 2) + 0.5);
// if (kh_value(h_mito, k) < 1) {
// kh_value(h_mito, k) = 1;
// } else if (kh_value(h_mito, k) > 6) {
// printf("Error: too many mitochondria contigs for node %d\n", node1);
// *flag_err = 1;
// return;
// }
// maxnum_mito += kh_value(h_mito, k);
// mt_uniq_len += ctg_depth[mt_contigs[i] - 1].len;
// // printf("ctg: %d, depth: %f, mt_uniq_len: %ld\n", mt_contigs[i], ctg_depth[mt_contigs[i] - 1].depth, mt_uniq_len);
// mt_uniq++;
// }
// }
for (i = 0; i < mt_num; i++) {
if (findint(pt_contigs, pt_num, mt_contigs[i]) == 0) {
int k = kh_put(node_num, h_mito, mt_contigs[i], &ret);
if (ret == 0) {
continue;
}
float denom = (mt_depth + min_depth) / 2;
if (denom <= 0) {
log_message(ERROR, "Invalid denominator for contig depth calculation.\n");
*flag_err = 1;
return;
}
kh_value(h_mito, k) = (int)(ctg_depth[mt_contigs[i] - 1].depth / denom + 0.5);
if (kh_value(h_mito, k) < 1) {
kh_value(h_mito, k) = 1;
// } else if (kh_value(h_mito, k) > 6) {
// printf("Error: Too many mitochondria contigs for node %d\n", node1);
// *flag_err = 1;
// return;
}
maxnum_mito += kh_value(h_mito, k);
mt_uniq_len += ctg_depth[mt_contigs[i] - 1].len;
mt_uniq++;
}
}
max_node = pt_num*5 + maxnum_mito + 1;
// for (k = kh_begin(h_mito); k != kh_end(h_mito); k++)
// {
// if (kh_exist(h_mito, k)) {
// log_info("%d: %d; ", kh_key(h_mito, k), kh_value(h_mito, k));
// }
// }
// log_info("\n");
/* Initialize chloroplast contig pass count to 0 */
for (i = 0; i < pt_num; i++)
{
k = kh_put(node_num, h_chloro, pt_contigs[i], &ret);
kh_value(h_chloro, k) = 0; // Initially, no chloroplast contig is passed
}
for (i = 0; i < mt_num; i++)
{
k = kh_put(Ha_nodedepth, h_depth, mt_contigs[i], &ret);
kh_value(h_depth, k) = ctg_depth[mt_contigs[i] - 1].depth;
}
g_sort_hash = h_depth;
/* Initialize h_links hash table */
if (mt_num == 1 && main_num == 1) {
nodeLink node_links;
node_links.node3num = 1;
node_links.node5num = 1;
node_links.node3 = (int*) malloc(1 * sizeof(int));
node_links.node3[0] = mt_contigs[0];
node_links.node3utr = (int*) malloc(1 * sizeof(int));
node_links.node3utr[0] = 5;
node_links.node5 = (int*) malloc(1 * sizeof(int));
node_links.node5[0] = mt_contigs[0];
node_links.node5utr = (int*) malloc(1 * sizeof(int));
node_links.node5utr[0] = 3;
k = kh_put(Ha_nodelink, h_links, mt_contigs[0], &ret);
kh_value(h_links, k) = node_links;
} else {
for (i = 0; i < mt_num; i++)
{
nodeLink node_links;
node_links.node3num = 0;
node_links.node5num = 0;
node_links.node3 = (int*) malloc(10 * sizeof(int));
node_links.node3utr = (int*) malloc(10 * sizeof(int));
node_links.node5 = (int*) malloc(10 * sizeof(int));
node_links.node5utr = (int*) malloc(10 * sizeof(int));
k = kh_put(Ha_nodelink, h_links, mt_contigs[i], &ret);
for (j = 0; j < main_num; j++)
{
if (mainlinks[j].lctgsmp == mt_contigs[i] || mainlinks[j].rctgsmp == mt_contigs[i]) {
if (mainlinks[j].lctgsmp == mt_contigs[i] && mainlinks[j].lutrsmp == 3) {
node_links.node3[node_links.node3num] = mainlinks[j].rctgsmp;
node_links.node3utr[node_links.node3num] = mainlinks[j].rutrsmp;
node_links.node3num++;
if (node_links.node3num >= 10) {
*flag_err = 1;
return;
}
} else if (mainlinks[j].rctgsmp == mt_contigs[i] && mainlinks[j].rutrsmp == 3) {
node_links.node3[node_links.node3num] = mainlinks[j].lctgsmp;
node_links.node3utr[node_links.node3num] = mainlinks[j].lutrsmp;
node_links.node3num++;
if (node_links.node3num >= 10) {
*flag_err = 1;
return;
}
} else if (mainlinks[j].lctgsmp == mt_contigs[i] && mainlinks[j].lutrsmp == 5) {
node_links.node5[node_links.node5num] = mainlinks[j].rctgsmp;
node_links.node5utr[node_links.node5num] = mainlinks[j].rutrsmp;
node_links.node5num++;
if (node_links.node5num >= 10) {
*flag_err = 1;
return;
}
} else {
node_links.node5[node_links.node5num] = mainlinks[j].lctgsmp;
node_links.node5utr[node_links.node5num] = mainlinks[j].lutrsmp;
node_links.node5num++;
if (node_links.node5num >= 10) {
*flag_err = 1;
return;
}
}
}
}
int* mttempnode5 = (int*)malloc(node_links.node5num * sizeof(int));
int* mttempnode5utr = (int*)malloc(node_links.node5num * sizeof(int));
int mtnode5num = 0;
int* pttempnode5 = (int*)malloc(node_links.node5num * sizeof(int));
int* pttempnode5utr = (int*)malloc(node_links.node5num * sizeof(int));
int ptnode5num = 0;
int* mttempnode3 = (int*)malloc(node_links.node3num * sizeof(int));
int* mttempnode3utr = (int*)malloc(node_links.node3num * sizeof(int));
int mtnode3num = 0;
int* pttempnode3 = (int*)malloc(node_links.node3num * sizeof(int));
int* pttempnode3utr = (int*)malloc(node_links.node3num * sizeof(int));
int ptnode3num = 0;
for (j = 0; j < node_links.node3num; j++) {
if (findint(pt_contigs, pt_num, node_links.node3[j]) == 0) {
mttempnode3[mtnode3num] = node_links.node3[j];
mttempnode3utr[mtnode3num] = node_links.node3utr[j];
mtnode3num++;
} else {
pttempnode3[ptnode3num] = node_links.node3[j];
pttempnode3utr[ptnode3num] = node_links.node3utr[j];
ptnode3num++;
}
}
for (j = 0; j < node_links.node5num; j++) {
if (findint(pt_contigs, pt_num, node_links.node5[j]) == 0) {
mttempnode5[mtnode5num] = node_links.node5[j];
mttempnode5utr[mtnode5num] = node_links.node5utr[j];
mtnode5num++;
} else {
pttempnode5[ptnode5num] = node_links.node5[j];
pttempnode5utr[ptnode5num] = node_links.node5utr[j];
ptnode5num++;
}
}
if (mtnode3num > 0) {
NodeUtrPair* mttempnode3pairs = (NodeUtrPair*)malloc(mtnode3num * sizeof(NodeUtrPair));
for (j = 0; j < mtnode3num; j++) {
mttempnode3pairs[j].node = mttempnode3[j];
mttempnode3pairs[j].utr = mttempnode3utr[j];
}
qsort(mttempnode3pairs, mtnode3num, sizeof(NodeUtrPair), compare_by_hash_value);
for (j = 0; j < mtnode3num; j++) {
mttempnode3[j] = mttempnode3pairs[j].node;
mttempnode3utr[j] = mttempnode3pairs[j].utr;
}
free(mttempnode3pairs);
}
if (mtnode5num > 0) {
NodeUtrPair* mttempnode5pairs = (NodeUtrPair*)malloc(mtnode5num * sizeof(NodeUtrPair));
for (j = 0; j < mtnode5num; j++) {
mttempnode5pairs[j].node = mttempnode5[j];
mttempnode5pairs[j].utr = mttempnode5utr[j];
}
qsort(mttempnode5pairs, mtnode5num, sizeof(NodeUtrPair), compare_by_hash_value);
for (j = 0; j < mtnode5num; j++) {
mttempnode5[j] = mttempnode5pairs[j].node;
mttempnode5utr[j] = mttempnode5pairs[j].utr;
}
free(mttempnode5pairs);
}
for (j = 0; j < node_links.node3num; j++) {
if (j < mtnode3num) {
node_links.node3[j] = mttempnode3[j];
node_links.node3utr[j] = mttempnode3utr[j];
} else {
node_links.node3[j] = pttempnode3[j - mtnode3num];
node_links.node3utr[j] = pttempnode3utr[j - mtnode3num];
}
}
for (j = 0; j < node_links.node5num; j++) {
if (j < mtnode5num) {
node_links.node5[j] = mttempnode5[j];
node_links.node5utr[j] = mttempnode5utr[j];
} else {
node_links.node5[j] = pttempnode5[j - mtnode5num];
node_links.node5utr[j] = pttempnode5utr[j - mtnode5num];
}
}
kh_value(h_links, k) = node_links;
}
}
pathScore path_score;
path_score.mt_nodenum = 0;
path_score.node_num = 0;
path_score.uniq_mt_nodenum = 0;
path_score.path_len = 0;
path_score.uniq_mt_pathlen = 0;
path_score.pt_nodenum = 10 * pt_num;
path_score.uniq_pt_nodenum = pt_num;
path_score.path_node = (int*)malloc((max_node) * sizeof(int));
path_score.path_utr = (int*)malloc((max_node) * sizeof(int));
path_score.type = 1;
path_score.inval_num = 0;
// nodePath current_path;
// current_path.nodenum = 1;
// current_path.node = (int*)malloc((max_node) * sizeof(int));
// current_path.node[0] = node1;
// current_path.utr = (int*)malloc((max_node) * sizeof(int));
// current_path.utr[0] = node1utr;
// current_path.nodelen = ctg_depth[node1 - 1].len;
// current_path.pathlen = 0;
// current_path.type = 1;
int cpu = 8;
mpath* bfs_path = (mpath*)malloc(2*cpu * sizeof(mpath));