Extra annotations to transcriptome-assembly.

1) use the main reference as a scaffold for newly assembled transcripts,
this keeps known gene_ids and transcript_ids and places novel transcripts
of a known gene_id on the known gene_id
2) broadly classify as lincRNA, ncRNA and protein_coding by training
a logistic model to classify non_coding and coding transcripts in
the known reference.
3) remove some Cufflinks specific garbage transcripts such as single exon
novel genes
Updated with work over the last month.
Throw error if fastq1 == fastq2 in the configuration file.
Remove cpat requirement until conda install has chance to propagate (heads up @roryk). Utility function to retrieve data dictionary from argument list
vardict development started
Vardict integrated into bcbio-nextgen
Vardict changes to accommodate empty files containing no variants
vardict development started
Fix to correctly pass paired.tumor_name
Merge pull request #514 from mjafin/master

VarDict integration in bcbio
Support new merge arguments in bedtools 2.20.1 (fixes #515). Provide ability to retrieve file extensions in general way. Update history with VarDict and add support to cancer tests
Tumour only calling using FreeBayes falls back to single sample mode
Calculate fastqc name to find after downsampling to ensure we correctly find files in downsampling applied. Fixes #512
Avoid division by zero error in cpat (fixes #517). Cleanly avoid running cpat if not installed
vcfallelicprimitives applied to paired FreeBayes output
Added FreeBayes tumor-only test
Avoid doing merging of input variant_regions BED files until required. Enables passing initial full files with extra fields through to VarDict and other callers that require them. Thanks to @mjafin @bioinfo
Merge pull request #518 from mjafin/freebayes

Tumour only calling using FreeBayes falls back to single sample mode
Support additional genomes: TAIR10 and WBcel235
Structural variation improvements: Delly downsampling to 50M reads, limit maximum callsize into ensemble/BED calls for validation. Handle CNV based matches