loadihashref parameter removal

CommandLineParser.c

@@ -97,7 +97,7 @@ int parseCommandLine (int argc, char *argv[])
   int o;
   int index;
   char *fastaFile = NULL;
-  
+
   readGroup[0] = 0;
   sampleName[0] = 0;
   libName[0] = 0;
@@ -118,6 +118,7 @@ int parseCommandLine (int argc, char *argv[])
       {"search",	required_argument,  0,			's'},
       {"help",		no_argument,	    0,			'h'},
       {"version",	no_argument,	    0,			'v'},
+      {"quiet",	        no_argument,	    0,			'q'},
       {"seq",		required_argument,  0,			'x'},
       {"seq1",		required_argument,  0,			'x'},
       {"seq2",		required_argument,  0,			'y'},
@@ -210,6 +211,10 @@ int parseCommandLine (int argc, char *argv[])
 	  fprintf(stderr, "mrFAST %s.%s with FastHASH\n", versionNumber, versionNumberF);
 	  return 0;
 	  break;				
+	case 'q':
+	  if (freopen("/dev/null", "w", stderr) == NULL)
+	    fprintf(stderr, "Quiet mode failure.\n");
+	  break;				
 	case '?': 
 	  fprintf(stderr, "Unknown parameter: %s\n", longOptions[index].name);
 	  abort();

HashTable.c

@@ -286,7 +286,7 @@ void finalizeLoadingIHashTable()
 }
 
 /**********************************************/
-int  loadIHashTable(double *loadTime, int errThreshould)
+int  loadIHashTable(double *loadTime)
 {
   double startTime = getTime();
   unsigned char extraInfo = 0;
@@ -426,7 +426,6 @@ int initLoadingHashTable(char *fileName)
 
   tmp = fread(&WINDOW_SIZE, sizeof(WINDOW_SIZE), 1, _ih_fp);
 
-  fprintf(stderr, "Hash table kmer length: %d\n", WINDOW_SIZE);
   configHashTable();
 
   if (_ih_maxHashTableSize != pow(4, WINDOW_SIZE))

HashTable.h

@@ -66,7 +66,7 @@ int				initLoadingHashTable(char *fileName);
 HashTable		*getHashTable();
 
 void 			(*generateHashTable)(char *fileName, char *indexName);
-int				(*loadHashTable)(double *loadTime, int errThreshould);
+int				(*loadHashTable)(double *loadTime);
 void			(*finalizeLoadingHashTable)();
 unsigned int	*(*getCandidates)(int hv);
 

baseFAST.c

@@ -172,7 +172,7 @@ int main(int argc, char *argv[])
 	  do
 	    {
 
-	      flag = loadHashTable ( &tmpTime, errThreshold);  			// Reading a fragment
+	      flag = loadHashTable ( &tmpTime);  			// Reading a fragment
 	      curGen = getRefGenomeName();
 
 	      // First Time
@@ -256,7 +256,7 @@ int main(int argc, char *argv[])
 	  do
 	    {
 
-	      flag = loadHashTable ( &tmpTime , errThreshold);  			// Reading a fragment
+	      flag = loadHashTable ( &tmpTime);  			// Reading a fragment
 	      curGen = getRefGenomeName();
 
 	      // First Time