Update delly filtering to use bcftools per-sample filtering. GATK genotype filtering does not work correctly with complex JEXL expressions
Fix detection of no coverage regions for chromosomes excluded by variant_regions. Thanks to Severine Catreux
Fix for extracting single-end FASTQ files from BAM.
Bump STAR minimum memory requirement to 40G.

It seems like .z4 uses slightly more memory.
Improved memory usage for larger numbers of sample or contigs: Do zipping of return messages through IPython, increase available GC sockets to IPython, and perform better downsampling of GATK calls. #386
Sailfish support added.

Very bare bones, for testing. Just runs Sailfish on a set of FASTQ files, needs
to have some QC information and to be run through bcbio.rnaseq to compare.
Sailfish install has some warts, so no installer support yet.
Provide support for gemini 0.7.0 and avoid CADD and gerp loads if not present in gemini database directory
Add picard to the RNA-seq alignment step.
Bump Picard max memory to 4g.
Initial framework for supporting effects calculation with Ensembl's variant effect predictor
Update resource files to support VEP and latest snpEff Ensembl databases. Enable VEP support in Gemini
Add RNA-seq example.
Use restructured text formatting for links.
Improve documentation for installation. Add recent bcbio nextgen presentation at Biogen
Enable support for dbNSFP and CADD data integration. dbNSFP integrates through an Ensembl VEP plugin and CADD through GEMINI database creation. #146
Improved flexibility on generating validation plots with mixed recalibration/realignment inputs. Fixes #438
Fix validation plot title generation for non-GATK and minimal inputs. Fixes #438
Improved documentation on adding pre-existing genomes to bcbio. #440
Improve snpEff version detection during installation to use manifest version if available. Thanks to Glen Otero
Allow . to be a pair-file separator.