cleanup

src/bedtools.cpp

@@ -210,7 +210,7 @@ int bedtools_help(void)
     cout  << "    random        "  << "Generate random intervals in a genome.\n";
     cout  << "    shuffle       "  << "Randomly redistrubute intervals in a genome.\n";
     cout  << "    sample        "  << "Sample random records from file using reservoir sampling.\n";   
-    cout  << "    spacing       "  << "Report the spacing between intervals in a file.\n";     
+    cout  << "    spacing       "  << "Report the gap lengths between intervals in a file.\n";     
     cout  << "    annotate      "  << "Annotate coverage of features from multiple files.\n";
     
     cout  << endl;

src/spacingFile/SpacingFile.cpp

@@ -52,7 +52,7 @@ bool SpacingFile::getSpacing()
 			{
 				// do curr and prev overlap?
 				if (curr->sameChromIntersects(prev, false, false, 1E-9, false))
-					distance.append(0);
+					distance.append(-1);
 				else
 					distance.append(curr->getStartPos() - prev->getEndPos());
 			}

src/spacingFile/spacingMain.cpp

@@ -37,14 +37,14 @@ void spacing_help(void) {
 
     cerr << "\nTool:    bedtools spacing" << endl;
     cerr << "Version: " << VERSION << "\n";
-    cerr << "Summary: Report (last col.) the length of the space between intervals." << endl << endl;
+    cerr << "Summary: Report (last col.) the gap lengths between intervals in a file." << endl << endl;
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf/bam>" << endl << endl;
     
     cerr << "Notes: " << endl;
     cerr << "\t(1)  Input must be sorted by chrom,start (sort -k1,1 -k2,2n for BED)." << endl;
     cerr << "\t(2)  The 1st element for each chrom will have NULL distance. (\".\")." << endl;
-    cerr << "\t(3)  The distance for both overlapping and bookended intervals is 0." << endl << endl;
+    cerr << "\t(3)  Distance for overlapping intervaks is -1 and bookended is 0." << endl << endl;
 
     cerr << "Example: " << endl;
     cerr << "\t$ cat test.bed " << endl;

src/split/splitBed.cpp

@@ -124,7 +124,7 @@ int BedSplit::main(int argc,char** argv)
         }
     if(num_chuncks<=0)
         {
-        cerr << "Error: num_chuncks==0.\n" << endl;
+        cerr << "Error: num_chunks==0.\n" << endl;
         usage(cerr);
         return EXIT_FAILURE;
         }
@@ -138,7 +138,7 @@ int BedSplit::main(int argc,char** argv)
         }
     else 
         {
-        cerr << "Unknow split algorithm " << algorithm << endl;
+        cerr << "Unknown split algorithm " << algorithm << endl;
         return EXIT_FAILURE;
         }
     }
@@ -151,6 +151,7 @@ std::FILE* BedSplit::saveFileChunk(std::string& filename,size_t file_index)
     sprintf(tmp,"%05d",(file_index+1));
     filename.append(".").append(tmp).append(".bed");
     FILE* out = fopen(filename.c_str(),"w");
+    
     if(out==NULL)
         {
         fprintf(stderr,"Cannot open \"%s\". %s\n",

src/split/splitBed.h

@@ -24,6 +24,7 @@
 // Class methods and elements
 //************************************************
 class BedSplit {
+
 private:
     std::string bedFileName;
     std::string outfileprefix;
@@ -37,10 +38,8 @@ private:
     void loadBed();
     int doSimpleSplit();
     int doEuristicSplitOnTotalSize();
-public:
-
-
 
+public:
     // constructor
     BedSplit();
     // destructor