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
Merge pull request #212 from lbeltrame/freebayes-somatic

Implementation of Freebayes tumor/normal calling
Add testing hook and history information for Luca's FreeBayes paired analysis contribution #212