Merge branch 'hotfix/1.13.1'

cancerit · Mar 10, 2018 · 635c7e2 · 635c7e2
2 parents 60a8d97 + e65da72
commit 635c7e2
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Showing 11 changed files with 31 additions and 27 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.13.1
+
+* Ensure all `sentinel` calls return non-zero exit code.
+
 ## 1.13.0
 
 * Overlapping reads now handled #78

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.0
+CAVEMAN_VERSION=1.13.1
 TEST_REF?=""
 #Compiler
 CC?=gcc

diff --git a/src/alg_bean.c b/src/alg_bean.c
@@ -93,7 +93,7 @@ alg_bean_t *alg_bean_read_file(FILE *file){
 			bean->lane = lanes_list;
 			bean->lane_size = List_count(lanes_list);
 		}else{
-			sentinel("Unrecognised id passed: %s.",text_id);
+			sentinel("Unrecognised id passed: %s.",text_id,1);
 		}
 	}
 

diff --git a/src/cn_access.c b/src/cn_access.c
@@ -142,7 +142,7 @@ int8_t cn_access_get_copy_number_for_location(char *file_loc,char *chr,uint32_t
       }
     }
 	}else{
-		sentinel("Somehow copy number for location %s:%d was not available.",chr,pos);
+		sentinel("Somehow copy number for location %s:%d was not available.",chr,pos,1);
 	}
 	return cn;
 error:

diff --git a/src/config_file_access.c b/src/config_file_access.c
@@ -77,7 +77,7 @@ int config_file_access_read_config_file(FILE *file, char *tum_bam_file, char *no
 			check(chk!=NULL,"Error retrieving CWD when reading config file.");
 			if(strcmp(cur_wd,value)!=0){
 				sentinel("Your current working directory '%s' is not the same as the directory you setup CaVEMan: '%s'. Please change to that directory and try again.",
-										cur_wd,value);
+										cur_wd,value,1);
 			}
 		}else if(strcmp(MUT_TUM,key)==0){
 			strcpy(tum_bam_file,value);
@@ -118,7 +118,7 @@ int config_file_access_read_config_file(FILE *file, char *tum_bam_file, char *no
 		}else if(strcmp(TUM_CN_KEY,key)==0){
 			strcpy(tum_cn,value);
 		}else{
-			sentinel("Unrecognised key in config file '%s'.",key);
+			sentinel("Unrecognised key in config file '%s'.",key,1);
 		}
 	}
 

diff --git a/src/estep.c b/src/estep.c
@@ -200,7 +200,7 @@ void estep_setup_options(int argc, char *argv[]){
 
       case 'M':
       	if(sscanf(optarg, "%i", &cn) != 1){
-      		sentinel("Error parsing -M argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -M argument '%s'. Should be an integer > 0",optarg,1);
       	}
         cn_access_set_max_cn(cn);
         break;
@@ -215,79 +215,79 @@ void estep_setup_options(int argc, char *argv[]){
 
       case 'n':
       	if(sscanf(optarg, "%i", &normal_copy_number) != 1){
-      		sentinel("Error parsing -n argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -n argument '%s'. Should be an integer > 0",optarg,1);
       	}
         break;
 
       case 't':
       	if(sscanf(optarg, "%i", &tumour_copy_number) != 1){
-      		sentinel("Error parsing -t argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -t argument '%s'. Should be an integer > 0",optarg,1);
       	}
         break;
 
       case 'i':
       	if(sscanf(optarg, "%i", &idx) != 1){
-      		sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg,1);
       	}
         break;
 
       case 'm':
       	if(sscanf(optarg, "%i", &min_bq) != 1){
-      		sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg);
+      		sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg,1);
       	}
         break;
 
 			case 'k':
 				if(sscanf(optarg, "%f", &norm_contam) != 1){
-      		sentinel("Error parsing -k argument '%s'. Should be a float >= 0.0.",optarg);
+      		sentinel("Error parsing -k argument '%s'. Should be a float >= 0.0.",optarg,1);
       	}
 				break;
 
 			case 'd':
 				if(sscanf(optarg, "%f", &prior_snp_prob) != 1){
-      		sentinel("Error parsing -d argument '%s'. Should be a float > 0.0.",optarg);
+      		sentinel("Error parsing -d argument '%s'. Should be a float > 0.0.",optarg,1);
       	}
 				break;
 
 			case 'c':
 				if(sscanf(optarg, "%f", &prior_mut_prob) != 1){
-      		sentinel("Error parsing -c argument '%s'. Should be a float > 0.0.",optarg);
+      		sentinel("Error parsing -c argument '%s'. Should be a float > 0.0.",optarg,1);
       	}
 				break;
 
 			case 'b':
 				if(sscanf(optarg, "%f", &ref_bias) != 1){
-      		sentinel("Error parsing -b argument '%s'. Should be a float >= 0.0.",optarg);
+      		sentinel("Error parsing -b argument '%s'. Should be a float >= 0.0.",optarg,1);
       	}
 				break;
 
 			case 'p':
 				if(sscanf(optarg, "%f", &min_mut_prob) != 1){
-      		sentinel("Error parsing -p argument '%s'. Should be a float >= 0.0.",optarg);
+      		sentinel("Error parsing -p argument '%s'. Should be a float >= 0.0.",optarg,1);
       	}
 				break;
 
 			case 'q':
 				if(sscanf(optarg, "%f", &min_snp_prob) != 1){
-      		sentinel("Error parsing -q argument '%s'. Should be a float >= 0.0.",optarg);
+      		sentinel("Error parsing -q argument '%s'. Should be a float >= 0.0.",optarg,1);
       	}
 				break;
 
 			case 'x':
 				if(sscanf(optarg, "%i", &min_tum_cvg) != 1){
-      		sentinel("Error parsing -x argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -x argument '%s'. Should be an integer > 0",optarg,1);
       	}
 				break;
 
 			case 'y':
 				if(sscanf(optarg, "%i", &min_norm_cvg) != 1){
-      		sentinel("Error parsing -y argument '%s'. Should be an integer > 0",optarg);
+      		sentinel("Error parsing -y argument '%s'. Should be an integer > 0",optarg,1);
       	}
 				break;
 
 			case 'a':
 				if(sscanf(optarg, "%i", &split_size) != 1){
-      		sentinel("Error parsing -a argument '%s'. Should be an integer >= 0",optarg);
+      		sentinel("Error parsing -a argument '%s'. Should be an integer >= 0",optarg,1);
       	}
 				break;
 

diff --git a/src/generateCavemanVCFUnmatchedNormalPanel.c b/src/generateCavemanVCFUnmatchedNormalPanel.c
@@ -321,7 +321,7 @@ List *gen_panel_get_list_of_samples_and_locs(){
 	bamchar = strtok(bam_file_locs,",");
 	LIST_FOREACH(samples, first, next, cur){
 		if(bamchar == NULL){
-			sentinel("List of sample names and bam locations are not equal in length.");
+			sentinel("List of sample names and bam locations are not equal in length.",1);
 		}
 		((sample_bam *)cur->value)->bam_file = malloc(sizeof(char) * (strlen(bamchar) + 1));
 		check_mem(((sample_bam *)cur->value)->bam_file);

diff --git a/src/genotype.c b/src/genotype.c
@@ -70,7 +70,7 @@ void genotype_add_base_to_count(genotype_t *geno, const char base){
 			break;
 
 		default:
-			sentinel("Incorrect base passed to add: %c",base);
+			sentinel("Incorrect base passed to add: %c",base,1);
 			break;
 	};
 	return;

diff --git a/src/ignore_reg_access.c b/src/ignore_reg_access.c
@@ -127,7 +127,7 @@ int ignore_reg_access_get_ign_reg_for_chr(char *ign_file,char *chr, int entry_co
 			}
 		}else{
 			free(chr_nom);
-			sentinel("Incorrect line read from ignore file %s.",rd);
+			sentinel("Incorrect line read from ignore file %s.",rd,1);
 		}
 		free(chr_nom);
 	}

diff --git a/src/mstep.c b/src/mstep.c
@@ -106,19 +106,19 @@ void mstep_setup_options(int argc, char *argv[]){
 
       	case 'i':
       		if(sscanf(optarg, "%i", &idx) != 1){
-      			sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg);
+      			sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg,1);
       		}
       		break;
 
       	case 'm':
       		if(sscanf(optarg, "%i", &min_bq) != 1){
-      			sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg);
+      			sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg,1);
       		}
       		break;
 
       	case 'a':
       		if(sscanf(optarg, "%i", &split_size) != 1){
-      			sentinel("Error parsing -a argument '%s'. Should be an integer > 0",optarg);
+      			sentinel("Error parsing -a argument '%s'. Should be an integer > 0",optarg,1);
       		}
 					break;
 

diff --git a/src/split.c b/src/split.c
@@ -102,13 +102,13 @@ void split_setup_options(int argc, char *argv[]){
 
       	case 'i':
       		if(sscanf(optarg, "%i", &idx) != 1){
-      			sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg);
+      			sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg,1);
       		}
       		break;
 
       	case 'e':
       		if(sscanf(optarg, "%i", &max_read_count) != 1){
-      			sentinel("Error parsing -e argument '%s'. Should be an integer > 0",optarg);
+      			sentinel("Error parsing -e argument '%s'. Should be an integer > 0",optarg,1);
       		}
       		break;
-Original file line number
+Diff line change
@@ Expand Up @@
           }
         }
     	}else{
-    		sentinel("Somehow copy number for location %s:%d was not available.",chr,pos);
+    		sentinel("Somehow copy number for location %s:%d was not available.",chr,pos,1);
     	}
     	return cn;
     error:
@@ Expand Down @@