From 55c05b07668010378a22e3881f7df81415ac4f32 Mon Sep 17 00:00:00 2001
From: Georgi Tushev <georgi.handzhiyski@gmail.com>
Date: Thu, 8 Sep 2016 00:11:54 +0200
Subject: [PATCH] add MAPQ filter settings

---
 config.c | 17 +++++++++++++----
 config.h |  4 +++-
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/config.c b/config.c
index c7499a2..1d5840d 100644
--- 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
index d0c0b8c..42e5498 100644
--- 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);