introduce uint64_t hash key concatenating chrome and base

MPIBR-Bioinformatics · Oct 13, 2016 · c7525ac · c7525ac
1 parent 49fd900
commit c7525ac
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Showing 5 changed files with 153 additions and 165 deletions.
diff --git a/config.c b/config.c
@@ -14,13 +14,10 @@ const char PROGRAM_NAME[] = "PASSFinder";
 void aux_init(aux_config_t *aux)
 {
     /* initialize default auxiliary values */
-    aux->input = NULL;
-    aux->polymask = NULL;
-    aux->output = NULL;
-    aux->window = AUX_DEFAULT_WINDOW;
-    aux->depth = AUX_DEFAULT_DEPTH;
+    aux->file_in = NULL;
+    aux->file_mask = NULL;
     aux->polysize = AUX_DEFAULT_POLYSIZE;
-    aux->maskspan = AUX_DEFAULT_MASKSPAN;
+    aux->masksize = AUX_DEFAULT_MASKSIZE;
     aux->mapq = AUX_DEFAULT_MAPQ;
 
     return;
@@ -50,46 +47,29 @@ int aux_parse(aux_config_t *aux, int argc, const char *argv[])
             i += 1;
             aux->mapq = (uint32_t)strtoul(argv[i], NULL, 10);
         }
-        else if((PARAMETER_CHECK("-w", 2, parameterLength)) || (PARAMETER_CHECK("--window", 8, parameterLength)))
-        {
-            i += 1;
-            aux->window = (uint32_t)strtoul(argv[i], NULL, 10);
-        }
-        else if((PARAMETER_CHECK("-d", 2, parameterLength)) ||
-                (PARAMETER_CHECK("--depth", 7, parameterLength)))
-        {
-            i += 1;
-            aux->depth = (uint32_t)strtoul(argv[i], NULL, 10);
-        }
         else if((PARAMETER_CHECK("-p", 2, parameterLength)) ||
                 (PARAMETER_CHECK("--polysize", 10, parameterLength)))
         {
             i += 1;
             aux->polysize = (uint32_t)strtoul(argv[i], NULL, 10);
         }
-        else if((PARAMETER_CHECK("-s", 2, parameterLength)) ||
-                (PARAMETER_CHECK("--maskspan", 10, parameterLength)))
+        else if((PARAMETER_CHECK("-m", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--masksize", 10, parameterLength)))
         {
             i += 1;
-            aux->maskspan = (uint32_t)strtoul(argv[i], NULL, 10);
+            aux->masksize = (uint32_t)strtoul(argv[i], NULL, 10);
         }
         else if((PARAMETER_CHECK("-i", 2, parameterLength)) ||
                 (PARAMETER_CHECK("--input", 7, parameterLength)))
         {
             i += 1;
-            aux->input = argv[i];
-        }
-        else if((PARAMETER_CHECK("-m", 2, parameterLength)) ||
-                (PARAMETER_CHECK("--maskpoly", 10, parameterLength)))
-        {
-            i += 1;
-            aux->polymask = argv[i];
+            aux->file_in = argv[i];
         }
-        else if((PARAMETER_CHECK("-o", 2, parameterLength)) ||
-                (PARAMETER_CHECK("--output", 8, parameterLength)))
+        else if((PARAMETER_CHECK("-r", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--regions", 10, parameterLength)))
         {
             i += 1;
-            aux->output = argv[i];
+            aux->file_mask = argv[i];
         }
         else
         {

diff --git a/config.h b/config.h
@@ -15,10 +15,8 @@
 
 // define some constants
 #define MAX_LENGTH 1024
-#define AUX_DEFAULT_WINDOW 200
-#define AUX_DEFAULT_DEPTH 5
 #define AUX_DEFAULT_POLYSIZE 3
-#define AUX_DEFAULT_MASKSPAN 3
+#define AUX_DEFAULT_MASKSIZE 3
 #define AUX_DEFAULT_MAPQ 0
 
 // define MIN & MAX macros
@@ -32,12 +30,9 @@
 // define parameters
 typedef struct _aux_config_t
 {
-    const char    *input;
-    const char    *polymask;
-    const char    *output;
-    uint32_t window;
-    uint32_t depth;
-    uint32_t maskspan;
+    const char    *file_in;
+    const char    *file_mask;
+    uint32_t masksize;
     uint32_t polysize;
     uint32_t mapq;
 } aux_config_t;