Update get_paired_bams to return a namedtuple if the analysis is paired, and None if there is missing metadata
Rename is_sample_pair to is_sample_analysis
Add support for Freebayes paired tumor/normal variant calling

Currently untested and not plugged into the main pipeline yet
Merge remote-tracking branch 'upstream/master' into freebayes-somatic
Adjust is_paired_analysis to proper return true or false
Correct get_paired_bams according to the review
Update the freebayes call according to review
Merge remote-tracking branch 'upstream/master' into freebayes-somatic

Conflicts:
	bcbio/variation/vcfutils.py
Detect paired samples and act accordingly (normal freebayes / paired freebayes)
Minor PEP8 fixes, add a docstring to the paired function
Add a comment telling that the order of the samples in the vcfsamplediff
call isn't arbitrary
Merge remote-tracking branch 'upstream/master' into freebayes-somatic
Fix calling logic (inverted calls!)
Fix the bam.index calls
Fix a misplaced indent
Add back the reference file to freebayes call
Handle torque/maui scheduler when queues do not map to associated nodes #236
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Docker work to get running test code: merge local docker bcbio_system files with global specified; handle remapping genome directories specified in external *.loc files when use relative paths; ensure environmental variables are correctly set.
Provide monitoring of run status. Utilitize in docker runner script to wait until finish prior to cleaning up docker resources
Provide stdout/stderr from docker run to original process by streaming docker logs.
Use provenance do.run for snpEff effect prediction, redirecting stdout via the shell instead of subprocess #237
Allow single string specification for upload directory, defaulting to local install. Thanks to Eva König