From 04bed568528adf0460943f45643a94cb8b3e0a71 Mon Sep 17 00:00:00 2001
From: Georgi Tushev <georgi.tushev@brain.mpg.de>
Date: Thu, 13 Sep 2018 15:07:17 +0200
Subject: [PATCH] fix seg.fault when wrong parameters

---
 config.c | 39 ++++++++++++++++++++-------------------
 config.h |  3 +--
 main.c   | 31 +++++++++++++------------------
 3 files changed, 34 insertions(+), 39 deletions(-)

diff --git a/config.c b/config.c
index 48c616b..76ffa69 100644
--- a/config.c
+++ b/config.c
@@ -11,7 +11,7 @@
 const char VERSION[] = "v0.01";
 const char PROGRAM_NAME[] = "PASSFinder";
 
-void aux_init(aux_config_t *aux)
+void aux_parse(aux_config_t *aux, int argc, const char *argv[])
 {
     /* initialize default auxiliary values */
     aux->file_in = NULL;
@@ -19,18 +19,21 @@ void aux_init(aux_config_t *aux)
     aux->polysize = AUX_DEFAULT_POLYSIZE;
     aux->masksize = AUX_DEFAULT_MASKSIZE;
     aux->mapq = AUX_DEFAULT_MAPQ;
-    
-    return;
-}
 
-int aux_parse(aux_config_t *aux, int argc, const char *argv[])
-{
+    if ((argc != 2) && (argc < 4))
+    {
+      fprintf(stderr, "Error: provide input, output and mask\n");
+      help();
+    }
+
+
     /* parse input pairs */
     for(int i = 1; i < argc; i++)
     {
+
         // current paramter length
         uint64_t parameterLength = strlen(argv[i]);
-        
+
         // check each parameter and its value
         if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
            (PARAMETER_CHECK("--help", 6, parameterLength)))
@@ -74,13 +77,11 @@ int aux_parse(aux_config_t *aux, int argc, const char *argv[])
         else
         {
             fprintf(stderr, "Error:: Unknown parameter %s\n", argv[i]);
-            return EXIT_FAILURE;
+            help();
         }
-        
-        
     }
 
-    return EXIT_SUCCESS;
+    return;
 }
 
 
@@ -88,27 +89,27 @@ int aux_parse(aux_config_t *aux, int argc, const char *argv[])
 void version(void)
 {
     fprintf(stderr, "PASSFinder %s\n", VERSION);
-    return;
+    exit(EXIT_SUCCESS);
 }
 
 void help(void)
 {
-    
+
     fprintf(stderr, "\nTool: PASSFinder\n");
     fprintf(stderr, "Version: %s\n", VERSION);
     fprintf(stderr, "Summary:\n");
     fprintf(stderr, "\tCluster PolyA supported sites from 3'End sequencing.\n");
     fprintf(stderr, "\nUsage:\t%s [OPTIONS] -i/--input <bam/stdin> -m/--maskpoly <bed> -o/--output <bed/stdout>\n", PROGRAM_NAME);
     fprintf(stderr, "Options:\n");
-    fprintf(stderr, "\t-i/--input BAM/stdin file\n");
-    fprintf(stderr, "\t-o/--output BED/stdout file\n");
-    fprintf(stderr, "\t-m/--maskpoly BED/stdin file with genomic poly regions\n");
+    fprintf(stderr, "\t-i/--input BAM/stdin file [required]\n");
+    fprintf(stderr, "\t-o/--output BED/stdout file [required]\n");
+    fprintf(stderr, "\t-m/--maskpoly BED/stdin file with genomic poly regions [required]\n");
     fprintf(stderr, "\t-w/--window\tsliding window size\n");
     fprintf(stderr, "\t-d/--depth\tminimum number of polyA reads to define PASS\n");
     fprintf(stderr, "\t-p/--polysize\tminimum number of As for tail and Ts for head to define poly stretch\n");
     fprintf(stderr, "\t-h/--help\tprint help message\n");
     fprintf(stderr, "\t-v/--version\tprint current version\n");
-    return;
+    exit(EXIT_SUCCESS);
 }
 
 int chomp(char *line_buf)
@@ -117,6 +118,6 @@ int chomp(char *line_buf)
     line_length = strlen(line_buf) - 1;
     if(line_buf[line_length] == '\n')
         line_buf[line_length] = '\0';
-    
+
     return 0;
-}
\ No newline at end of file
+}
diff --git a/config.h b/config.h
index 7d3776f..2ba9434 100644
--- a/config.h
+++ b/config.h
@@ -39,8 +39,7 @@ typedef struct _aux_config_t
 } aux_config_t;
 
 // function declarations
-void aux_init(aux_config_t *);
-int aux_parse(aux_config_t *, int, const char **);
+void aux_parse(aux_config_t *, int, const char **);
 void help(void);
 void version(void);
 int chomp(char *);
diff --git a/main.c b/main.c
index f10e9c1..d6197a8 100644
--- a/main.c
+++ b/main.c
@@ -16,35 +16,30 @@ int main(int argc, const char * argv[])
 {
     aux_config_t aux;
     hts_config_t hts;
-    
-    clock_t begin = clock();
-    
+
+
     // parse auxiliary configuration
-    aux_init(&aux);
-    if (aux_parse(&aux, argc, argv))
-    {
-        help();
-        return EXIT_FAILURE;
-    }
-    
+    aux_parse(&aux, argc, argv);
+
+    clock_t begin = clock();
+
     // initialize with hts
     hts_init(&hts, &aux);
-    
+
     // parse with hts
     hts_parse(&hts, &aux);
-    
+
     // dump hash
     hts_printout(&hts);
-    
+
     // free
     hts_destroy(&hts);
-    
-    
+
     clock_t end = clock();
-    
+
     double time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
-    
+
     fprintf(stderr, "Time: %.4f sec\n", time_spent);
-    
+
     return 0;
 }