Merge branch 'hotfix/1.13.2'

cancerit · Mar 15, 2018 · 6bba096 · 6bba096
2 parents 635c7e2 + 3f789df
commit 6bba096
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Showing 15 changed files with 71 additions and 55 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 1.13.2
+
+* Futher fixes for `sentinel` calls.
+* * Correct versin of REQUIRED_MIN_LIBZ as we are looking for greater than.
+
 ## 1.13.1
 
 * Ensure all `sentinel` calls return non-zero exit code.

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-CAVEMAN_VERSION=1.13.1
+CAVEMAN_VERSION=1.13.2
 TEST_REF?=""
 #Compiler
 CC?=gcc

diff --git a/setup.sh b/setup.sh
@@ -23,7 +23,7 @@
 
 SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2"
 
-REQUIRED_MIN_LIBZ="1.2.3.5"
+REQUIRED_MIN_LIBZ="1.2.3.4"
 
 function version_gt() { test "$(printf '%s\n' "$@" | sort -V | head -n 1)" != "$1"; }
 

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,1);
+			sentinel("Unrecognised id passed: %s.",text_id);
 		}
 	}
 

diff --git a/src/algos.c b/src/algos.c
@@ -708,22 +708,24 @@ int algos_estep_read_position(alg_bean_t *alg,long double ********prob_arr, char
 				}
 				//read_pos_t struct has copy number and ref base is a usable base.
 				if(pos->ref_base_idx >= 0 && pos->norm_cn > 0 && pos->tum_cn > 0){
+					int chk = 0;
 					//Adding to the counts at this position.
 					if(pos_t->normal == 1){
 						if(pos_t->strand == 1){
-							genotype_add_base_to_count(pos->norm_rev_cvg,toupper(seq_nt16_str[pos_t->called_base]));
+							chk = genotype_add_base_to_count(pos->norm_rev_cvg,toupper(seq_nt16_str[pos_t->called_base]));
 						}else{
-							genotype_add_base_to_count(pos->norm_fwd_cvg,toupper(seq_nt16_str[pos_t->called_base]));
+							chk = genotype_add_base_to_count(pos->norm_fwd_cvg,toupper(seq_nt16_str[pos_t->called_base]));
 						}
 						pos->total_cvg_norm++;
 					}else if(pos_t->normal == 0){
 						if(pos_t->strand == 1){
-							genotype_add_base_to_count(pos->tum_rev_cvg,toupper(seq_nt16_str[pos_t->called_base]));
+							chk = genotype_add_base_to_count(pos->tum_rev_cvg,toupper(seq_nt16_str[pos_t->called_base]));
 						}else{
-							genotype_add_base_to_count(pos->tum_fwd_cvg,toupper(seq_nt16_str[pos_t->called_base]));
+							chk = genotype_add_base_to_count(pos->tum_fwd_cvg,toupper(seq_nt16_str[pos_t->called_base]));
 						}
 						pos->total_cvg_tum++;
 					}
+					check(chk==0,"Error adding genotype to base count.");
 					//Get the index for things we'll use during analysis
 					int rpos_i,mq_i,bq_i,callbase_i;
 					int ok = algos_get_read_specific_indices(alg,pos_t,&rpos_i,&mq_i,&bq_i,&callbase_i);

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,1);
+		sentinel("Somehow copy number for location %s:%d was not available.",chr,pos);
 	}
 	return cn;
 error:

diff --git a/src/config_file_access.c b/src/config_file_access.c
@@ -76,8 +76,7 @@ int config_file_access_read_config_file(FILE *file, char *tum_bam_file, char *no
 			char *chk = getcwd(cur_wd,size);
 			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,1);
+				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);
 			}
 		}else if(strcmp(MUT_TUM,key)==0){
 			strcpy(tum_bam_file,value);
@@ -118,7 +117,7 @@ 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,1);
+			sentinel("Unrecognised key in config file '%s'.",key);
 		}
 	}
 

diff --git a/src/estep.c b/src/estep.c
@@ -122,7 +122,7 @@ void estep_print_usage (int exit_code){
   exit(exit_code);
 }
 
-void estep_setup_options(int argc, char *argv[]){
+int estep_setup_options(int argc, char *argv[]){
 	const struct option long_opts[] =
 	{
              	{"config-file", required_argument, 0, 'f'},
@@ -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,1);
+      		sentinel("Error parsing -M argument '%s'. Should be an integer > 0",optarg);
       	}
         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,1);
+      		sentinel("Error parsing -n argument '%s'. Should be an integer > 0",optarg);
       	}
         break;
 
       case 't':
       	if(sscanf(optarg, "%i", &tumour_copy_number) != 1){
-      		sentinel("Error parsing -t argument '%s'. Should be an integer > 0",optarg,1);
+      		sentinel("Error parsing -t argument '%s'. Should be an integer > 0",optarg);
       	}
         break;
 
       case 'i':
       	if(sscanf(optarg, "%i", &idx) != 1){
-      		sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg,1);
+      		sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg);
       	}
         break;
 
       case 'm':
       	if(sscanf(optarg, "%i", &min_bq) != 1){
-      		sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg,1);
+      		sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg);
       	}
         break;
 
 			case 'k':
 				if(sscanf(optarg, "%f", &norm_contam) != 1){
-      		sentinel("Error parsing -k argument '%s'. Should be a float >= 0.0.",optarg,1);
+      		sentinel("Error parsing -k argument '%s'. Should be a float >= 0.0.",optarg);
       	}
 				break;
 
 			case 'd':
 				if(sscanf(optarg, "%f", &prior_snp_prob) != 1){
-      		sentinel("Error parsing -d argument '%s'. Should be a float > 0.0.",optarg,1);
+      		sentinel("Error parsing -d argument '%s'. Should be a float > 0.0.",optarg);
       	}
 				break;
 
 			case 'c':
 				if(sscanf(optarg, "%f", &prior_mut_prob) != 1){
-      		sentinel("Error parsing -c argument '%s'. Should be a float > 0.0.",optarg,1);
+      		sentinel("Error parsing -c argument '%s'. Should be a float > 0.0.",optarg);
       	}
 				break;
 
 			case 'b':
 				if(sscanf(optarg, "%f", &ref_bias) != 1){
-      		sentinel("Error parsing -b argument '%s'. Should be a float >= 0.0.",optarg,1);
+      		sentinel("Error parsing -b argument '%s'. Should be a float >= 0.0.",optarg);
       	}
 				break;
 
 			case 'p':
 				if(sscanf(optarg, "%f", &min_mut_prob) != 1){
-      		sentinel("Error parsing -p argument '%s'. Should be a float >= 0.0.",optarg,1);
+      		sentinel("Error parsing -p argument '%s'. Should be a float >= 0.0.",optarg);
       	}
 				break;
 
 			case 'q':
 				if(sscanf(optarg, "%f", &min_snp_prob) != 1){
-      		sentinel("Error parsing -q argument '%s'. Should be a float >= 0.0.",optarg,1);
+      		sentinel("Error parsing -q argument '%s'. Should be a float >= 0.0.",optarg);
       	}
 				break;
 
 			case 'x':
 				if(sscanf(optarg, "%i", &min_tum_cvg) != 1){
-      		sentinel("Error parsing -x argument '%s'. Should be an integer > 0",optarg,1);
+      		sentinel("Error parsing -x argument '%s'. Should be an integer > 0",optarg);
       	}
 				break;
 
 			case 'y':
 				if(sscanf(optarg, "%i", &min_norm_cvg) != 1){
-      		sentinel("Error parsing -y argument '%s'. Should be an integer > 0",optarg,1);
+      		sentinel("Error parsing -y argument '%s'. Should be an integer > 0",optarg);
       	}
 				break;
 
 			case 'a':
 				if(sscanf(optarg, "%i", &split_size) != 1){
-      		sentinel("Error parsing -a argument '%s'. Should be an integer >= 0",optarg,1);
+      		sentinel("Error parsing -a argument '%s'. Should be an integer >= 0",optarg);
       	}
 				break;
 
@@ -341,15 +341,16 @@ void estep_setup_options(int argc, char *argv[]){
 
    set_max_tum_cvg(estep_max_tumour_coverage);
 
-   return;
+   return 0;
 
 error:
 	estep_print_usage (1);
-	return;
+	return -1;
 }
 
 int estep_main(int argc, char *argv[]){
-	estep_setup_options(argc, argv);
+	int is_err = estep_setup_options(argc, argv);
+	check(is_err==0, "Error parsing options");
 
 	long double ********prob_arr = NULL;
 	alg_bean_t *alg = NULL;

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.",1);
+			sentinel("List of sample names and bam locations are not equal in length.");
 		}
 		((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
@@ -50,7 +50,7 @@ List *genotype_hard_copy_genotype_t_list(List *new_list, List *old){
 	return new_list;
 }
 
-void genotype_add_base_to_count(genotype_t *geno, const char base){
+int genotype_add_base_to_count(genotype_t *geno, const char base){
 	assert(geno != NULL);
 	switch(base){
 		case 'A':
@@ -70,12 +70,12 @@ void genotype_add_base_to_count(genotype_t *geno, const char base){
 			break;
 
 		default:
-			sentinel("Incorrect base passed to add: %c",base,1);
+			sentinel("Incorrect base passed to add: %c",base);
 			break;
 	};
-	return;
+	return 0;
 error:
-	return;
+	return -1;
 }
 
 void genotype_set_base_count(genotype_t *geno, const char base, int count){
@@ -226,14 +226,16 @@ List *genotype_calculate_genotypes(int copy_num, char *ref_base){
          	//Create 2 copies, one will be reference, the next will be mutant base.
          	genotype_t *gen1 = genotype_copy_genotype(gen);
          	genotype_t *gen2 = genotype_copy_genotype(gen1);
-         	genotype_add_base_to_count(gen2,ref_base[0]);
+         	int chk = genotype_add_base_to_count(gen2,ref_base[0]);
+					check(chk==0,"Error adding base to genotype count.");
          	List_push(tmp,gen2);
          	int j=0;
       		for(j=0; j<4; j++){
       			int base_count = genotype_get_base_count(gen1,bases[j]);
       			check(base_count >= 0, "Error fetching base count for base: %c with genotype: %s.",bases[j],genotype_get_genotype_t_as_string(gen1));
 						if(base_count>=1 && ref_base[0] != bases[j]){
-							genotype_add_base_to_count(gen1,bases[j]);
+							chk = genotype_add_base_to_count(gen1,bases[j]);
+							check(chk==0,"Error adding base to genotype count.");
 							List_push(tmp,gen1);
 						}
       		}
@@ -247,7 +249,8 @@ List *genotype_calculate_genotypes(int copy_num, char *ref_base){
       	for(j=0; j<4; j++){
       		genotype_t *gen = genotype_init_genotype();
       		check(gen != NULL, "Error generating genotype.");
-      		genotype_add_base_to_count(gen,bases[j]);
+      		int chk = genotype_add_base_to_count(gen,bases[j]);
+					check(chk==0,"Error adding base to genotype count.");
       		List_push(genos,gen);
       	}
       }

diff --git a/src/genotype.h b/src/genotype.h
@@ -78,7 +78,7 @@ List *genotype_calculate_genotypes(int copy_num, char *ref_base);
 char *genotype_get_genotype_t_as_string(genotype_t *geno);
 long double genotype_get_var_base_proportion(genotype_t *gen, char ref_base, int copy_num);
 char genotype_get_var_base(genotype_t *geno, char ref_base);
-void genotype_add_base_to_count(genotype_t *geno, char base);
+int genotype_add_base_to_count(genotype_t *geno, char base);
 int genotype_get_base_count(genotype_t *geno, char base);
 void genotype_set_base_count(genotype_t *geno, char base, int count);
 int genotype_get_total_base_count(genotype_t *geno);

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,1);
+			sentinel("Incorrect line read from ignore file %s.",rd);
 		}
 		free(chr_nom);
 	}

diff --git a/src/mstep.c b/src/mstep.c
@@ -78,7 +78,7 @@ void mstep_print_usage (int exit_code){
   exit(exit_code);
 }
 
-void mstep_setup_options(int argc, char *argv[]){
+int mstep_setup_options(int argc, char *argv[]){
 	const struct option long_opts[] =
 	{
 		         {"config-file", required_argument, 0, 'f'},
@@ -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,1);
+      			sentinel("Error parsing -i argument '%s'. Should be an integer > 0",optarg);
       		}
       		break;
 
       	case 'm':
       		if(sscanf(optarg, "%i", &min_bq) != 1){
-      			sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg,1);
+      			sentinel("Error parsing -m argument '%s'. Should be an integer >= 0",optarg);
       		}
       		break;
 
       	case 'a':
       		if(sscanf(optarg, "%i", &split_size) != 1){
-      			sentinel("Error parsing -a argument '%s'. Should be an integer > 0",optarg,1);
+      			sentinel("Error parsing -a argument '%s'. Should be an integer > 0",optarg);
       		}
 					break;
 
@@ -144,15 +144,16 @@ void mstep_setup_options(int argc, char *argv[]){
    	mstep_print_usage(1);
    }
 
-   return;
+   return 0;
 
 error:
 	mstep_print_usage (1);
-	return;
+	return -1;
 }
 
 int mstep_main(int argc, char *argv[]){
-	mstep_setup_options(argc,argv);
+	int is_err = mstep_setup_options(argc,argv);
+	check(is_err==0, "Error parsing options.");
 
 	char *fa_file = NULL;
 	uint64_t ********arr_check = NULL;