Add a note that read names ending by /1 /2 or /3 are consdered different by pairedBamToBed12.
Convert the internal documentation to POD format.
Add help option in addition to "usage"; die after printing help.
Export the POD documentation and link to it for nice display in GitHub.
Also refresh the plain text readme with the Makefile.
Merge pull request #3 from charles-plessy/master

Add a note that read names ending by /1 /2 or /3 are consdered different by pairedBamToBed12.