add MAPQ filter settings

MPIBR-Bioinformatics · Sep 7, 2016 · 55c05b0 · 55c05b0
1 parent dacb22d
commit 55c05b0
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Showing 2 changed files with 16 additions and 5 deletions.
diff --git a/config.c b/config.c
@@ -11,7 +11,7 @@
 const char VERSION[] = "v0.01";
 const char PROGRAM_NAME[] = "FastPASSFinder";
 
-int parseSettings(int argc, char *argv[], Settings *config)
+int parseSettings(int argc, const char *argv[], Settings *config)
 {
     // initialize default values
     config->input = NULL;
@@ -20,6 +20,7 @@ int parseSettings(int argc, char *argv[], Settings *config)
     config->window = DEFAULT_WINDOW;
     config->depth = DEFAULT_DEPTH;
     config->sizepoly = DEFAULT_SIZEPOLY;
+    config->mapq = DEFAULT_MAPQ;
 
     if(argc < 5)
     {
@@ -44,6 +45,17 @@ int parseSettings(int argc, char *argv[], Settings *config)
         {
             version();
         }
+        else if((PARAMETER_CHECK("-q", 2, parameterLength)) || (PARAMETER_CHECK("--mapq", 6, parameterLength)))
+        {
+            i += 1;
+            config->mapq = strtol(argv[i], NULL, 10);
+
+            if (config->mapq < 0)
+            {
+                fprintf(stderr, "Error:: MAPQ should be >=0!\n");
+                return EXIT_FAILURE;
+            }
+        }
         else if((PARAMETER_CHECK("-w", 2, parameterLength)) || (PARAMETER_CHECK("--window", 8, parameterLength)))
         {
             i += 1;
@@ -85,7 +97,6 @@ int parseSettings(int argc, char *argv[], Settings *config)
                 (PARAMETER_CHECK("--input", 7, parameterLength)))
         {
             i += 1;
-
             config->input = argv[i];
 
             if (config->input == NULL)
@@ -98,7 +109,6 @@ int parseSettings(int argc, char *argv[], Settings *config)
                 (PARAMETER_CHECK("--maskpoly", 10, parameterLength)))
         {
             i += 1;
-
             config->maskpoly = argv[i];
 
             if (config->maskpoly == NULL)
@@ -112,7 +122,6 @@ int parseSettings(int argc, char *argv[], Settings *config)
                 (PARAMETER_CHECK("--output", 8, parameterLength)))
         {
             i += 1;
-
             config->output = argv[i];
 
             if (config->output == NULL)

diff --git a/config.h b/config.h
@@ -18,6 +18,7 @@
 #define DEFAULT_WINDOW 200
 #define DEFAULT_DEPTH 5
 #define DEFAULT_SIZEPOLY 3
+#define DEFAULT_MAPQ 0
 
 // define MIN & MAX macros
 #define MIN(a,b) (((a)<(b))?(a):(b))
@@ -36,11 +37,12 @@ typedef struct _Settings
     int64_t window;
     int64_t depth;
     int64_t sizepoly;
+    int64_t mapq;
 } Settings;
 
 // function declarations
 int chompNewLine(char *);
-int parseSettings(int, char **, Settings *);
+int parseSettings(int, const char **, Settings *);
 int help(void);
 int version(void);