Add --strand-filter 1 to VarScan somatic options

This is done in order to filter variants with extremely high (>90%)
strand bias.
Fix Tophat inner distance calculation.

Read pairs  spanning exons cause outliers in the insert size
distribution. This uses the median and an estimate
of the standard deviation based on the median absolute
deviation which is more stable w.r.t outliers.
Update with RNA-seq changes.
Provide infrastructure to run caller-based ensemble combines from multiple inputs. Uses the bcbio.variation.recall toolkit. Still a work in progress
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Merge pull request #310 from lbeltrame/add-strand-bias-varscan

Add --strand-filter 1 to VarScan somatic options
Fix race conditions in QC generation, handling partially completed results and simultaneous runs on the same file. Fixes #311
Speed improvements for job re-runs. Remove checking steps inside main output file checkpoints. #299
Add function to only return mapped reads from a BAM file.
Remove the merge SAM and FASTQ step after alignment.

STAR has an option to output the unmapped reads and Tophat
has a separate BAM file of unmapped reads. Both need to have
the read groups fixed on them, and Tophat has some additional
issues where the flags are not set properly on unmapped
mate pairs.
Finish writing the docstring for _fix_unmapped.
Handle in-place data dictionary updates from alignment as well as raw SAM output.
Remove unused function.
Support for latest bcftools and htslib release candidate: 0.2.0-rc6. Fixes #301
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add more helpful error message for bcbio installations where we cannot find data directory. Fixes #313
Add star attribute to test.

Now we can test Tophat and STAR separately.
Add more in depth description of the RNA-seq output.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Generalize reference detection to provide pointers for fasta files, reference indexes, plus aligner indexes. Enables shipping full analysis to non-shared filesystem by enumerating all requirements