Merge branch 'hotfix/1.13.16'

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.13.16
+
+* Correct occasional memory blowout caused by split step not excluding an ignore region.
+
 ## 1.13.15
 
 * Add checks to sam_iter_next to ensure result is checked for errors

Makefile

@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.15
+CAVEMAN_VERSION=1.13.16
 
 TEST_REF?=""
 #Compiler

src/ignore_reg_access.c

@@ -40,156 +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;
+     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);
-	check(li != NULL,"Error fetching contained ignore regions.");
+    List *li = ignore_reg_access_get_ign_regs_covered(start,end,regions,entry_count);
+    check(li != NULL,"Error fetching contained ignore regions.");
 
-	List *reg_for_analysis = List_create();
-	seq_region_t *range = malloc(sizeof(struct seq_region_t));
-	range->beg = start;
-	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;
+    List *reg_for_analysis = List_create();
+    seq_region_t *range = malloc(sizeof(struct seq_region_t));
+
+    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);
+        }
+    }
+    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);
+     }
 }

src/ignore_reg_access.h

@@ -47,7 +47,7 @@ int ignore_reg_access_get_ign_reg_count_for_chr(char *ign_file,char *chr);
 int ignore_reg_access_get_ign_reg_for_chr(char *ign_file,char *chr,int entry_count,struct seq_region_t **regions);
 seq_region_t *ignore_reg_access_get_ign_reg_overlap(int pos, struct seq_region_t **regions, int entry_count);
 void ignore_reg_access_destroy_seq_region_t_arr(int entry_count, struct seq_region_t **regions);
-List *ignore_reg_access_get_ign_reg_contained(int from, int to, struct seq_region_t **regions, int entry_count);
+List *ignore_reg_access_get_ign_regs_covered(int from, int to, struct seq_region_t **regions, int entry_count);
 List *ignore_reg_access_resolve_ignores_to_analysis_sections(int from, int to, struct seq_region_t **regions, int entry_count);
 
 #endif