Mark the feature as experimental, release it as version 1.2.

See the previous commits for the implementation.  Closes #4.

RELEASE_HISTORY

@@ -1,3 +1,8 @@
+Version 1.2 (August 15th, 2015, codename chassé-croisé)
+
+Added an experimental -extraG option to correct for G-mismatches on the first
+base, found in CAGE libraries.
+
 Version 1.1 (July 14th, 2016, codename Cocorico!)
 
 Added a -nsep option to only compare read names up to a common separator

src/pairedBamToBed12/pairedBamToBed12.cpp

@@ -38,8 +38,9 @@ using namespace BamTools;
 
 using namespace std;
 
-// define our program name
+// define our program name and version
 #define PROGRAM_NAME "pairedBamToBed12"
+#define PROGRAM_VERSION "1.2"
 
 // define our parameter checking macro
 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
@@ -165,7 +166,7 @@ int pairedbamtobed12_main(int argc, char* argv[]) {
 
 void pairedbamtobed12_help(void) {
 
-    cerr << "\nTool:    pairedBamToBed12 1.1" << endl;
+    cerr << "\nTool:    " << PROGRAM_NAME << " " << PROGRAM_VERSION << endl;
     cerr << "Summary: Converts 'properly paired' BAM alignments to BED12 format." << endl;
     cerr << "         Typically producing a 2 blocks BED12 entry for each 'properly paired' BAM pair." << endl;
     cerr << "         Additional blocks are produced when an alignment contains long deletion (CIGAR N-op)." << endl;
@@ -177,7 +178,7 @@ void pairedbamtobed12_help(void) {
 
     cerr << "\t-dblock\t"  << "Triggers the creation of a new block when an alignment contains short deletion from reference (CIGAR D-op)" << endl << endl;
 
-    cerr << "\t-extraG\t"  << "Ignore G mismatches on first bases (for use on CAGE alignments with BWA aln)." << endl << endl;
+    cerr << "\t-extraG\t"  << "Ignore G mismatches on first bases (experimental, for use on CAGE alignments with BWA aln)." << endl << endl;
 
     cerr << "\t-color\t"   << "An R,G,B string for the color used with BED12 format." << endl;
     cerr                   << "\t\tDefault is (255,0,0)." << endl << endl;