Merge tag '1.13.12' into dev

* Correct bad malloc on sscanf.

Conflicts:
	CHANGES.md

CHANGES.md

@@ -4,6 +4,10 @@
 
 * Making species and assembly required commandline arguments in the estep
 
+## 1.13.12
+
+* Correct bad malloc on sscanf.
+
 ## 1.13.11
 
 * Modify `fai_access_get_count_length_all_contigs` to use `strtok` rather than sscanf.

Makefile

@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.11
+CAVEMAN_VERSION=1.13.12
 
 TEST_REF?=""
 #Compiler

src/cn_access.c

@@ -59,7 +59,7 @@ int cn_access_populate_cn(char *file_loc,uint8_t is_normal){
 	char rd[250];
 	while(fgets(rd, 250, cn_file) != NULL){
 		check(rd != NULL,"Invalid line read in ignored region file.");
-		char *chr_nom = malloc(sizeof(char *));
+		char *chr_nom = malloc(sizeof(char) * 250);
 		int beg,end;
 		int chk = sscanf(rd,"%s\t%d\t%d\t%d",chr_nom,&beg,&end,&cop);
 		check(chk == 4,"Incorrect line parsed from copy number file.\n");

src/ignore_reg_access.c

@@ -105,7 +105,7 @@ int ignore_reg_access_get_ign_reg_for_chr(char *ign_file,char *chr, int entry_co
 	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);
+		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);

src/split_access.c

@@ -78,7 +78,7 @@ List *split_access_get_all_split_sections(char *file_loc){
 
 	while ( fgets(line,sizeof(line),file) != NULL ){
 		i++;
-		chr = malloc(sizeof(char) * 50);
+		chr = malloc(sizeof(char) * 250);
 		check_mem(chr);
 		int start_zero_based = 0;
 		int stop = 0;