Tweak HaplotypeCaller workarounds for GATK 2.5-2
Update setup.py requirement versions to match requirements.txt. Fixes pysam 0.7 problem. Thanks to @brentp
Add graphics for region selection strategy for parallel processing
Added a namespace for collecting file format tools.

These types of functions are sprinkled around, making them
hard to find/reuse, maybe collecting them in one spot is good.

Also included a decorator to check for file types to remove
some of the is-this-file-of-the-right-format-if-not-bail
boilerplate.
Added a bam -> chromosome sizes converter.
Changed output extension for bam -> sizes conversion.
Added converter from bam -> chromosome length sizes for freec.
Fixed bam2sam import.
Provide ability to customize program resources for specific samples. Use customization to pass array of specific options to novoalign
Use default novoalign treatment of multiple mapping reads unless otherwise configured
Ensure lane information is not selected for configuration when querying arguments
Update cluster documentation diagram with correct formula for cores created in multicore mode
Scheduler must be specified if using -t ipython.
Removed unused imports.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen