Add SOMATIC flag for FreeBayes records

Initial step to address issue #317, but it is not hooked yet to the pipeline
Merge branch 'master' into vcf-somatic-fix
Hook the somatic fixing to Freebayes's paired pipeline and make the move
be in place
Update bcbio_nextgen.py

I think the example configuration file has changed.
Update installation.rst

Fix typo in docs.
Merge pull request #367 from hammer/patch-1

Update bcbio_nextgen.py
Added @hammer
Merge pull request #368 from hammer/patch-2

Update installation.rst, thanks to @hammer
Update README.rst

My Mount Sinai affiliation probably makes more sense for contributions to this project!
Merge pull request #369 from hammer/patch-1

Update README.rst
HaplotypeCaller: ensure depth annotated in output VCFs and turn on GATK 3.1 hardware optimizations
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Improve automated tests to include mapping reads in chr22. Enables multi-chromosome and chromosome exclusion tests #370
Ensure extra haplotype chromosomes excluded from analysis regions if found in non-callable blocks. Avoids calling in these regions if not in variant_regions. Fixes #370
Update main.py

By default on Mac OS X the maximum number of files a process can open is 10,240. Unless the number 50,000 was chosen for a good reason, I suggest we change `target_procs` to `10240` to ensure a better out-of-the-box experience for Mac users.

The alternative would be to add a check for OS X before lowering `target_procs`.
Merge pull request #372 from hammer/patch-1

Mac OS X: use a lower value of target_procs
Ensure process setting handled correctly when maximum limits are infinite
Only pass on and perform ploidy evaluation during haploid conversion if output has a genotype call. Fixes #370
Prepare combined fastq files from a flowcell, merging samples on multiple lanes and outputs split by bcl2fastq. Create final configuration file describing samples for processing. Update galaxy upload to handle inputs provided through YAML configuration instead of directly via nglims calls.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen