Fix edge cases for updated callable calculation: contigs with no mapped reads and high coverage regions
Scalpel integration: provide clean skip if scalpel not installed. Clean up pep8 formatting. #432
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
Merge branch 'master' into vardict
VarDict paired mode introduced