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
Allow gathering torque machine info from command line.
Added quality trimming and fusion evaluation.
Handle mapping of input directories from sample YAML files into mounted docker locations
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Fix paired bam detection in qc.
Merge pull request #235 from porterjamesj/patch-1

Fix paired bam detection in qc.

Thanks @porterjamesj!
Fix improper cufflinks directory file creation.

Thanks to @porterjamesj.

Closes part of https://github.com/chapmanb/bcbio-nextgen/issues/234.