Add REJECT filter to non-somatic records in VarScan2

Like the work done in FreeBayes, this patch adds a REJECT filter to
non-somatic records (i.e., everything with a Somatic Status - SS - not
equal to 2) produced by VarScan2.

It includes some duplicated code from FreeBayes, which could be moved to
vcfutils.
pass extra args (for example, --pdb) to the testrunner
Merge pull request #450 from jwm/testrunner_passthrough_extra_args

pass extra args (for example, --pdb) to the testrunner
fix for #451
Wrap some of the longer lines.
Return BAM file if merge is called with just one file.
Added reference-guided transcriptome assembly with Cufflinks.
Generalize memoru scheduling to handle single core memory intensive processes alongside multi-CPU runs. Avoids overscheduling memory when programs do not run multicore and are using multiple cores for other programs
Merge pull request #452 from kern3020/master

fix for #451
Use toolz.get_in to get genome_resources/variation and dbsnp file. Fixes #451. Fixes #452
Add assemble_transcripts to allowed keywords in algorithm section.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Rework parallelization in variant calling to use more multicore steps. Avoid overcomitting large memory to tools like snpEff, GATK VQSR and bcbio-variation-recall if not used. Allow passing options to VEP to test single transcript support.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update installation.rst

add --data to dbnsfp download
Create combined FPKM file for all samples.

Also fixes a Cufflinks issue with FPKM being calculated twice for
isoforms with the same gene id when there is no overlap between
the two isoforms.
Mutect: default to Scalpel instead of SID. Scalpel: use less stringent settings for calling indels.
Merge pull request #455 from tanglingfung/patch-3

Update installation.rst
Merge pull request #456 from mjafin/master

Mutect: default to Scalpel instead of SID. Scalpel: use less stringent s...
Ensure joint recalling preparation directories shared when run on muiltiple machines