first cut at tuxedo tools specific pipeline
bugfixes for tuxedo pipeline
Don't index bam file in tuxedo pipeline
Use data.get instead of data[]
add min_read_length to ALGORITHM_KEYS
Remove B run  trimming.
Finalize removal of old brun trimming: removes supplemental code that is no longer used. Plug min_read_length into read_through_trimming. Add documentation. #267

Conflicts:
	HISTORY.md
	bcbio/bam/trim.py
	setup.py
Fix filename length bug in template workflow.
add cutadapt to used progs
Conflicts:
	bcbio/distributed/ipython.py