Created a help page for BaseCounter. It is incomplete

docs/tools/BaseCounter.md

+# BaseCounter 
+
+## Introduction
+This tool will generate Base count based on a bam file and a refflat file
+
+## Example
+Help menu
+~~~~
+Usage: BaseCounter [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -r <file> | --refFlat <file>
+        refFlat file. Mandatory
+  -o <directory> | --outputDir <directory>
+        Output directory. Mandatory
+  -b <file> | --bam <file>
+        Bam file. Mandatory
+  -p <prefix> | --prefix 
+  
+ ~~~~
+