new features landed
new features landed

In this commit we land several working, but incomplete features.

VCF output - complete but not 100% to spec, need to sort out some output
filtering issues, decide whether to output all possible genotypes per
sample or only the most likely.

Automatic sample name reading from BAM file headers - If no sample list
is passed on program invocation, BamBayes will assume that all read
groups in the input alignment file should be used in the analysis.
(read groups are signified by the @RG header and are equivalent in scope
to samples).

ekg/freebayes,nh13/freebayes,gkno/freebayes,nh13/freebayes,ekg/freebayes,nh13/freebayes,godotgildor/freebayes,gkno/freebayes,godotgildor/freebayes,gkno/freebayes,nh13/freebayes,godotgildor/freebayes,gkno/freebayes,nh13/freebayes,godotgildor/freebayes,ekg/freebayes,ekg/freebayes,gkno/freebayes,ekg/freebayes,godotgildor/freebayes