Allow overriding of the datadict generated getter/setter functions.

If you explicitly set a get_x or set_x function, it will not be
overwritten. This lets special complicated cases get handled inside
there without changing the function signature everywhere.

Fix to allow for .gff and .gff3 extensions for the DEXseq file.
Addresses an issue raised in #653.
Run vcffixup following vcfallelicprimitives to prevent introduction of problematic AN INFO fields. Fixes #674
Swap RNA-seq to use the datadict indirection.
Add data dictionary iterator.

This is a little cleaner-looking than doing stuff like sample[0][0].
Move RNA-seq to use the data dictionary iterator.
Structural variation calling: finalize WHAM conversion to BED files and inclusion in ensemble calls. Fixes for plotting validated SV calls with seaborn
Delly speed improvement: ensure parallel cores passed to CombineVariants
Improved structural variant ensemble calling: collapse overlapping calls by size group to avoid a big influence from large calls. More flexible matching of wham outputs
Ensure local R site library injected when finding DEXSeq location. Handle GFF retrieval when no GTF file in DEXSeq unit tests. Fixes #653
Remove stray print statement.
Avoid passing exclude file for LUMPY SV calling if empty. Fixes #676
Avoid using bam_index_build2 (BAM indexing with specification of output bai file) since not supported in samtools 1.1 (samtools/samtools#199). Fixes #653
Remove problem calls in output LUMPY VCF with empty alleles. Fixes #678
Update move instead of copy to work around issue on some filesystems. Fixes #677
Alternative fix for problem LUMPY calls with no reference allele -- convert to Ns instead of dropping. #678
Move disambiguation split work inside parallel framework so download and preparation occurs on worker nodes or inside Docker containers. Enables on demand download of disambiguation genomes.
Allow use of pre-aligned input files into lumpy, assuming correct bwa-mem alignment. Fixes #682
Do not keep INFO and FORMAT fields when splitting complex alleles, reverting previous change introduced in v0.8.3. vcfallelicprimitives produces invalid VCF fields not resolved by vcffixup and will take more to include in the future. Fixes #679. Fixes #675
Fix for not uploading the combined files at the end of a RNA-seq run.
Add eXpress support.

http://bio.math.berkeley.edu/eXpress/overview.html