fixes spelling mistake cf PR #9

README.md

@@ -187,27 +187,28 @@ MindTheGap is composed of two main modules : breakpoint detection (`find` module
     
     * `-nb-cores`: number of cores to be used for computation [default '0', ie. all available cores will be used].
     * `-max-memory`: max RAM memory for the graph creation (in MBytes)  [default '2000']. Increasing the memory will speed up the graph creation phase.
-    * `-max-disk`: max usable disk space for the graph creation (in MBytes)  [default '0', ie. automatically set]. Kmers are counted by writting temporary files on the disk, to speed up the counting you can increase the usable disk space.
+    * `-max-disk`: max usable disk space for the graph creation (in MBytes)  [default '0', ie. automatically set]. Kmers are counted by writing temporary files on the disk, to speed up the counting you can increase the usable disk space.
     
 4. **MindTheGap Output**
 
     All the output files are prefixed either by a default name: "MindTheGap_Expe-[date:YY:MM:DD-HH:mm]" or by a user defined prefix (option `-out` of MindTheGap).
     Both MindTheGap modules generate the graph file if reads were given as input: 
-    * a graph file (`.h5`). This is a binary file, to obtain information stored in it, you can use the utility program `dbginfo` located in your bin directory or in ext/gatb-core/bin/.
-
+    
+* a graph file (`.h5`). This is a binary file, to obtain information stored in it, you can use the utility program `dbginfo` located in your bin directory or in ext/gatb-core/bin/.
+    
     `MindTheGap find` generates the following output files:
     * a breakpoint file (`.breakpoints`) in fasta format. 
-    * a variant file (`.othervariants.vcf`) in vcf format. It contains SNPs and deletion events.
-
+* a variant file (`.othervariants.vcf`) in vcf format. It contains SNPs and deletion events.
+    
     `MindTheGap fill` generates the following output files:
-    * a sequence file (`.insertions.fasta`) in fasta format. It contains the inserted sequences or contig gap-fills that were successfully assembled. 
-
-    * an insertion variant file (`.insertions.vcf`) in vcf format, in the case of insertion variant detection. 
-
-    * an assembly graph file (`.gfa`) in GFA format, in the case of contig gap-filling. It contains the original contigs and the obtained gap-fill sequences (nodes of the graph), together with their overlapping relationships (arcs of the graph).
-
-    * a log file (`.info.txt`), a tabular file with some information about the filling process for each breakpoint/grap-fill. 
-
+* a sequence file (`.insertions.fasta`) in fasta format. It contains the inserted sequences or contig gap-fills that were successfully assembled. 
+    
+* an insertion variant file (`.insertions.vcf`) in vcf format, in the case of insertion variant detection. 
+    
+* an assembly graph file (`.gfa`) in GFA format, in the case of contig gap-filling. It contains the original contigs and the obtained gap-fill sequences (nodes of the graph), together with their overlapping relationships (arcs of the graph).
+    
+* a log file (`.info.txt`), a tabular file with some information about the filling process for each breakpoint/grap-fill. 
+    
       
 
 Other optional parameters and details on input and output file formats are given in [doc/MindTheGap_insertion_caller.md](doc/MindTheGap_insertion_caller.md) and [doc/MindTheGap_assembly.md](doc/MindTheGap_assembly.md), depending on the usage.

src/Filler.cpp

@@ -227,14 +227,14 @@ void Filler::execute ()
     _insert_file_name = getInput()->getStr(STR_URI_OUTPUT)+".insertions.fasta";
     _insert_file = fopen(_insert_file_name.c_str(), "w");
     if(_insert_file == NULL){
-        string message = "Cannot open file "+ _insert_file_name + " for writting";
+        string message = "Cannot open file "+ _insert_file_name + " for writing";
         throw Exception(message.c_str());
     }
 
     _insert_info_file_name = getInput()->getStr(STR_URI_OUTPUT)+".info.txt";
     _insert_info_file = fopen(_insert_info_file_name.c_str(), "w");
     if(_insert_info_file == NULL){
-        string message = "Cannot open file "+ _insert_info_file_name + " for writting";
+        string message = "Cannot open file "+ _insert_info_file_name + " for writing";
         throw Exception(message.c_str());
     }
 
@@ -245,8 +245,8 @@ void Filler::execute ()
         _vcf_file_name = getInput()->getStr(STR_URI_OUTPUT)+".insertions.vcf";
         _vcf_file = fopen(_vcf_file_name.c_str(), "w");
         if(_vcf_file == NULL){
-            //cerr <<" Cannot open file "<< _output_file <<" for writting" << endl;
-            string message = "Cannot open file "+ _vcf_file_name + " for writting";
+            //cerr <<" Cannot open file "<< _output_file <<" for writing" << endl;
+            string message = "Cannot open file "+ _vcf_file_name + " for writing";
             throw Exception(message.c_str());
         }
         writeVcfHeader();
@@ -259,7 +259,7 @@ void Filler::execute ()
         _gfa_file_name = getInput()->getStr(STR_URI_OUTPUT)+".gfa";
         _gfa_file = fopen(_gfa_file_name.c_str(),"w");
         if(_gfa_file == NULL){
-            string message = "Cannot open file "+ _gfa_file_name + " for writting";
+            string message = "Cannot open file "+ _gfa_file_name + " for writing";
             throw Exception(message.c_str());
         }
     }
@@ -1004,7 +1004,7 @@ void Filler::writeFilledBreakpoint(std::vector<filled_insertion_t>& filledSequen
         osolu_i <<   "solution " <<    it->solution_rank << "/" << it->solution_count ;
         string solu_i = it->solution_count >1 ?  osolu_i.str() : "" ;
 
-        //Writting sequence header
+        //writing sequence header
         if(_breakpointMode) //-bkpt mode, to keep the same header name as before
         {
             fprintf(_insert_file,">%s_len_%d_qual_%i_avg_cov_%.2f_median_cov_%.2f   %s\n",
@@ -1022,7 +1022,7 @@ void Filler::writeFilledBreakpoint(std::vector<filled_insertion_t>& filledSequen
             fprintf(_insert_file,"%s",insertionName.c_str());
         }
 
-        //Writting DNA sequence
+        //writing DNA sequence
         fprintf(_insert_file,"%.*s\n",(int)llen,insertion.c_str() );
 
 //        if(it->solution_count >1)

src/Finder.cpp

@@ -281,16 +281,16 @@ void Finder::execute ()
     _breakpoint_file_name = getInput()->getStr(STR_URI_OUTPUT)+".breakpoints";
     _breakpoint_file = fopen(_breakpoint_file_name.c_str(), "w");
     if(_breakpoint_file == NULL){
-        //cerr <<" Cannot open file "<< _output_file <<" for writting" << endl;
-        string message = "Cannot open file "+ _breakpoint_file_name + " for writting";
+        //cerr <<" Cannot open file "<< _output_file <<" for writing" << endl;
+        string message = "Cannot open file "+ _breakpoint_file_name + " for writing";
         throw Exception(message.c_str());
     }
 
     _vcf_file_name = getInput()->getStr(STR_URI_OUTPUT)+".othervariants.vcf";
     _vcf_file = fopen(_vcf_file_name.c_str(), "w");
     if(_vcf_file == NULL){
-    	//cerr <<" Cannot open file "<< _output_file <<" for writting" << endl;
-    	string message = "Cannot open file "+ _vcf_file_name + " for writting";
+    	//cerr <<" Cannot open file "<< _output_file <<" for writing" << endl;
+    	string message = "Cannot open file "+ _vcf_file_name + " for writing";
     	throw Exception(message.c_str());
     }
     writeVcfHeader();