added note about sorted input.

src/spacingFile/spacingMain.cpp

+/*
+ * spacingMain.cpp
+ *
+ *  Created on: Jan 15, 2015
+ *      Author: Aaron Quinlan
+ */
+
+#include <iostream>
+#include "ContextSpacing.h"
+#include "SpacingFile.h"
+
+#define PROGRAM_NAME "bedtools spacing"
+
+void spacing_help(void);
+
+int spacing_main(int argc, char **argv)
+{
+    ContextSpacing *context = new ContextSpacing();
+    if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+        if (!context->getErrorMsg().empty()) {
+            cerr << context->getErrorMsg() << endl;
+        }
+        spacing_help();
+        delete context;
+        return 1;
+    }
+    SpacingFile *spacingFile = new SpacingFile(context);
+
+    bool retVal = spacingFile->getSpacing();
+    delete spacingFile;
+    delete context;
+    return retVal ? 0 : 1;
+
+}
+
+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 << "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 << "Example: " << endl;
+    cerr << "\t$ cat test.bed " << endl;
+    cerr << "\tchr1    0   10 " << endl;
+    cerr << "\tchr1    10  20 " << endl;
+    cerr << "\tchr1    21  30 " << endl;
+    cerr << "\tchr1    35  45 " << endl;
+    cerr << "\tchr1    100 200 " << endl << endl;
+
+    cerr << "\t$ bedtools spacing -i test.bed " << endl;
+    cerr << "\tchr1    0   10  . " << endl;
+    cerr << "\tchr1    10  20  0 " << endl;
+    cerr << "\tchr1    21  30  1 " << endl;
+    cerr << "\tchr1    35  45  5 " << endl;
+    cerr << "\tchr1    100 200 55 " << endl << endl;
+
+    // end the program here
+    exit(1);
+}