Skip to content

Commit

Permalink
Changes to ignore_reg_access_get_ign_regs_covered from ignore_reg_acc…
Browse files Browse the repository at this point in the history 
…ess_get_ign_reg_contained. Changed logic in ignore_reg_access_resolve_ignores_to_analysis_sections
  • Loading branch information
David Jones committed Oct 25, 2019
1 parent f661b78 commit 377a5fc
Showing 1 changed file with 134 additions and 157 deletions.
291 changes: 134 additions & 157 deletions src/ignore_reg_access.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,189 +40,166 @@
#include <ignore_reg_access.h>

int ignore_reg_access_get_ign_reg_count_for_chr(char *ign_file, char *chr){
assert(ign_file != NULL);
assert(chr != NULL);
FILE *file = fopen(ign_file,"r");
check(file != NULL,"Couldn't open ignored region file: %s.",ign_file);
//Read all lines, only including the ones that are of the correct chromosome in the count
int entry_count = 0;
//read and count
char rd[200];
while(fgets(rd, 200, file) != NULL){
check(rd != NULL,"Invalid line read in ignored region file.");
char *chr_nom = malloc(sizeof(char)*50);
check_mem(chr_nom);
int chk = sscanf(rd,"%s",chr_nom);
check(chk == 1,"Incorrect line read.\n");
if(strcmp(chr_nom,chr) == 0){
entry_count++;
}
free(chr_nom);
}
check(fclose(file)==0,"Error closing ignored region file '%s'.",ign_file);
return entry_count;
assert(ign_file != NULL);
assert(chr != NULL);
FILE *file = fopen(ign_file,"r");
check(file != NULL,"Couldn't open ignored region file: %s.",ign_file);
//Read all lines, only including the ones that are of the correct chromosome in the count
int entry_count = 0;
//read and count
char rd[200];
while(fgets(rd, 200, file) != NULL){
check(rd != NULL,"Invalid line read in ignored region file.");
char *chr_nom = malloc(sizeof(char)*50);
check_mem(chr_nom);
int chk = sscanf(rd,"%s",chr_nom);
check(chk == 1,"Incorrect line read.\n");
if(strcmp(chr_nom,chr) == 0){
entry_count++;
}
free(chr_nom);
}
check(fclose(file)==0,"Error closing ignored region file '%s'.",ign_file);
return entry_count;
error:
if(file) fclose(file);
return -1;
}

seq_region_t *ignore_reg_access_get_ign_reg_inside(int pos, struct seq_region_t **regions, int entry_count){
int i=0;
for(i=0; i<entry_count; i++){
if(regions[i]->beg < pos && regions[i]->end > pos){
seq_region_t *reg_copy = malloc(sizeof(struct seq_region_t));
check_mem(reg_copy);
reg_copy->beg = regions[i]->beg;
reg_copy->end = regions[i]->end;
return reg_copy;
}
}
error:
return NULL;
if(file) fclose(file);
return -1;
}

seq_region_t *ignore_reg_access_get_ign_reg_overlap(int pos, struct seq_region_t **regions, int entry_count){
int i=0;
for(i=0; i<entry_count; i++){
if(regions[i]->beg <= pos && regions[i]->end >= pos){
seq_region_t *reg_copy = malloc(sizeof(struct seq_region_t));
check_mem(reg_copy);
reg_copy->beg = regions[i]->beg;
reg_copy->end = regions[i]->end;
return reg_copy;
}
}
int i=0;
for(i=0; i<entry_count; i++){
if(regions[i]->beg <= pos && regions[i]->end >= pos){
seq_region_t *reg_copy = malloc(sizeof(struct seq_region_t));
check_mem(reg_copy);
reg_copy->beg = regions[i]->beg;
reg_copy->end = regions[i]->end;
return reg_copy;
}
}
error:
return NULL;
return NULL;
}

int ignore_reg_access_get_ign_reg_for_chr(char *ign_file,char *chr, int entry_count, struct seq_region_t **regions){
assert(ign_file != NULL);
assert(chr != NULL);
assert(entry_count >= 0);
assert(sizeof(regions)>0);
int is_bed = 0;
if(entry_count == 0){
return 0;
}
//assign the right size to the array
//then reread so we can parse the actual lines.
//Check for bed extension
const char *ext = strrchr(ign_file, '.');
if(ext && ext != ign_file && strcmp(ext+1,"bed")==0){
is_bed = 1;
}
assert(ign_file != NULL);
assert(chr != NULL);
assert(entry_count >= 0);
assert(sizeof(regions)>0);
int is_bed = 0;
if(entry_count == 0){
return 0;
}
//assign the right size to the array
//then reread so we can parse the actual lines.
//Check for bed extension
const char *ext = strrchr(ign_file, '.');
if(ext && ext != ign_file && strcmp(ext+1,"bed")==0){
is_bed = 1;
}

FILE *file = fopen(ign_file,"r");
check(file != NULL,"Couldn't open ignored region file: %s.",ign_file);
int found_count = 0;
FILE *file = fopen(ign_file,"r");
check(file != NULL,"Couldn't open ignored region file: %s.",ign_file);
int found_count = 0;

char rd[200];
while(fgets(rd, 200, file) != NULL){
check(rd != NULL,"Invalid line read in ignored region file.");
char *chr_nom = malloc(sizeof(char)*250);
check_mem(chr_nom);
int beg,end;
int chk = sscanf(rd,"%s\t%d\t%d",chr_nom,&beg,&end);
if(chk==3){
if(strcmp(chr_nom,chr) == 0){
regions[found_count] = malloc(sizeof(struct seq_region_t));
check_mem(regions[found_count]);
regions[found_count]->beg = beg + is_bed;
regions[found_count]->end = end;
found_count++;
}
}else if(1==sscanf(rd,"%s",chr_nom)){//Check for just a chromosome.
if(strcmp(chr_nom,chr) == 0){
regions[found_count] = malloc(sizeof(struct seq_region_t));
check_mem(regions[found_count]);
regions[found_count]->beg = 1;
regions[found_count]->end = INT_MAX;
found_count++;
}
}else{
free(chr_nom);
sentinel("Incorrect line read from ignore file %s.",rd);
}
free(chr_nom);
}
check(entry_count == found_count,"Wrong number of lines found %d for chr: %s. Expected %d.",found_count,chr,entry_count);
check(fclose(file)==0,"Error closing ignored region file '%s'.",ign_file);
return 0;
char rd[200];
while(fgets(rd, 200, file) != NULL){
check(rd != NULL,"Invalid line read in ignored region file.");
char *chr_nom = malloc(sizeof(char)*250);
check_mem(chr_nom);
int beg,end;
int chk = sscanf(rd,"%s\t%d\t%d",chr_nom,&beg,&end);
if(chk==3){
if(strcmp(chr_nom,chr) == 0){
regions[found_count] = malloc(sizeof(struct seq_region_t));
check_mem(regions[found_count]);
regions[found_count]->beg = beg + is_bed;
regions[found_count]->end = end;
found_count++;
}
}else if(1==sscanf(rd,"%s",chr_nom)){//Check for just a chromosome.
if(strcmp(chr_nom,chr) == 0){
regions[found_count] = malloc(sizeof(struct seq_region_t));
check_mem(regions[found_count]);
regions[found_count]->beg = 1;
regions[found_count]->end = INT_MAX;
found_count++;
}
}else{
free(chr_nom);
sentinel("Incorrect line read from ignore file %s.",rd);
}
free(chr_nom);
}
check(entry_count == found_count,"Wrong number of lines found %d for chr: %s. Expected %d.",found_count,chr,entry_count);
check(fclose(file)==0,"Error closing ignored region file '%s'.",ign_file);
return 0;

error:
if(file) fclose(file);
if(regions) ignore_reg_access_destroy_seq_region_t_arr(entry_count, regions);
return -1;
if(file) fclose(file);
if(regions) ignore_reg_access_destroy_seq_region_t_arr(entry_count, regions);
return -1;
}

List *ignore_reg_access_get_ign_reg_contained(int from, int to, struct seq_region_t **regions, int entry_count){
List *li = List_create();
int i=0;
for(i=0; i<entry_count; i++){
if(regions[i]->beg >= from && regions[i]->end <= to){
//Make a copy of this region and put in the list
seq_region_t *reg_copy = malloc(sizeof(struct seq_region_t));
check_mem(reg_copy);
reg_copy->beg = regions[i]->beg;
reg_copy->end = regions[i]->end;
List_push(li,reg_copy);
}
}
return li;
List *ignore_reg_access_get_ign_regs_covered(int from, int to, struct seq_region_t **regions, int entry_count){
List *li = List_create();
int i=0;
for(i=0; i<entry_count; i++){
//Check if the ignore region overlaps this sequence section
if((from >= regions[i]->beg && from <= regions[i]->end) ||
(to >= regions[i]->beg && to <= regions[i]->end) ||
from <= regions[i]->beg && to >= regions[i]->end){
seq_region_t *reg_copy = malloc(sizeof(struct seq_region_t));
check_mem(reg_copy);
reg_copy->beg = regions[i]->beg;
reg_copy->end = regions[i]->end;
List_push(li,reg_copy);
} //End of checking if this ignore region overlaps
}
return li;
error:
return NULL;
return NULL;
}

List *ignore_reg_access_resolve_ignores_to_analysis_sections(int start, int end, struct seq_region_t **regions, int entry_count){
List *li = ignore_reg_access_get_ign_reg_contained(start,end,regions,entry_count);
List *li = ignore_reg_access_get_ign_regs_covered(start,end,regions,entry_count);
check(li != NULL,"Error fetching contained ignore regions.");
// Test for start overlap
seq_region_t *start_overlap = ignore_reg_access_get_ign_reg_inside(start, regions, entry_count);

//Test for end overlap
seq_region_t *stop_overlap = ignore_reg_access_get_ign_reg_inside(end, regions, entry_count);

List *reg_for_analysis = List_create();
seq_region_t *range = malloc(sizeof(struct seq_region_t));
if(start_overlap != NULL){
range->beg = start_overlap->end+1;
}else{
range->beg = start;
}
List *reg_for_analysis = List_create();
seq_region_t *range = malloc(sizeof(struct seq_region_t));

LIST_FOREACH(li, first, next, cur){
range->end = ((seq_region_t *) cur->value)->beg - 1;
List_push(reg_for_analysis,range);
range = malloc(sizeof(struct seq_region_t));
range->beg = ((seq_region_t *) cur->value)->end + 1;
}

if(stop_overlap != NULL){
if(stop_overlap->end+1 > end){
sentinel("Error in resolving ignored regions. End %d was lower than the end of the region %d\n",end,stop_overlap->end+1);
range->beg = start;
if(List_count(li) > 0){
if(start >= ((seq_region_t *) li->first->value)->beg){
range->beg = ((seq_region_t *) li->first->value)->end+1;
List_unshift(li);
}
range->end = stop_overlap->end+1;
}else{
range->end = end;
}
List_push(reg_for_analysis,range);
List_clear_destroy(li);
return reg_for_analysis;
LIST_FOREACH(li, first, next, cur){
range->end = ((seq_region_t *) cur->value)->beg - 1;
List_push(reg_for_analysis,range);
range = malloc(sizeof(struct seq_region_t));
range->beg = ((seq_region_t *) cur->value)->end + 1;
}

range->end = end;
List_push(reg_for_analysis,range);
List_clear_destroy(li);
return reg_for_analysis;
error:
List_clear_destroy(li);
return NULL;
List_clear_destroy(li);
return NULL;

}

void ignore_reg_access_destroy_seq_region_t_arr(int entry_count, seq_region_t **regions){
if(sizeof(regions) > 0){
int i=0;
for(i=0;i<entry_count;i++){
if(regions[i] != NULL){
free(regions[i]);
}
}
free(regions);
}
if(sizeof(regions) > 0){
int i=0;
for(i=0;i<entry_count;i++){
if(regions[i] != NULL){
free(regions[i]);
}
}
free(regions);
}
}

0 comments on commit 377a5fc

Please sign in to comment.