Merge pull request #51 from lozybean/master

Merge pull request #53 from lozybean/hotfix

fix interpreter mismatch; #ISSUE 52

enable basename.bai index for basename.bam bamfile

Merge pull request #50 from rbonneville/master

Add python shebang lines

Run dos2unix on source files

Document how to build RepeatFinder

Merge remote-tracking branch 'upstream/master'

Merge pull request #3 from rbonneville/iss039

Merge pull request #2 from rbonneville/iss021

Merge pull request #1 from rbonneville/iss010

README.md: change hyphen to dash in example

mantis.py: fix extension-preserving logic for paths without an extension. Fixes #39.

Merge pull request #36 from rbonneville/iss032