Remove too-small reads for single-end RNA-seq experiments.

Thanks to @mistrm82 for the report.
Merge pull request #543 from lpantano/upstream

add docs for qsignature and kraken, and remove E321(PEP8) from qsignatur...
Fixes for matplotlib error.

When some functions are getting pickled and sent to the engines,
I think what is happening is that is the first time matplotlib
has been imported on the engine even though it has been imported
at the top-level bcbio-nextgen process. So we have to set it to
use 'Agg' as the backend. We also set it to force the creation
of a new backend, which might work to wipe out a stale matplotlib
backend that is looking for a display.

Also bonus trailing space removal issues.

Thanks to @chapmanb, @lpantano and @mistrm82 for figuring out what
was up. Unless this didn't fix it, then no thanks.
Full framework support for GATK 3.x joint recalling approach. Needs a bit of additional refactoring to supporting multiple simultaneous variant calling and joint calling approaches before documenting and making fully supported (#348)
Add LC_ALL export required for Delly CentOS5 binary on newer systems
Switch default backend of matplotlib to 'agg' in the rc file.
Enable running joint recalling with multiple approaches simultaneously. Provide documentation for use in development version #348
Document addition of joint calling in history file
Fixes for pre-aligned input: ensure BAM index creation after de-duplication (#545). Ensable fixing of incorrect BAM quality scores by specifying 'illumina' for 'quality_format' (thanks to Craig Bohrson).
Add support for SNAP aligner indexes
Support germline variant detection with Platypus caller for both batch and joint calling approaches
fix syntax error
Merge pull request #546 from kern3020/master

fix syntax error
Add configuration for evaluating joint calling, platypus and SNAP. Small fixes to SNAP sorting memory usage to leave enough for alignment
Pin cutadapt to version 1.5.
Fix single-end progress message for STAR.
Subsetting a gzipped FASTQ file for testing fixed.

It was outputting uncompressed FASTQ files that had an extension of
.gz. This fixes that behavior by adding a gzip file opener that
will do the right thing if it is a gzipped file.
Merge upstream changes
Merge branch 'lpantano-upstream'
Initial cancer calling evaluation using DREAM challenge synthetic dataset 3