v1.1.9

• Fix for get VEP cache.
• Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).
• Remove mitochondrial reads from ChIP/ATAC-seq calling.
• Add documentation describing ATAC-seq outputs.
• Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report
  (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics)
• Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks
  to @naumenko-sa for the intial implementation and push to get this going.
• Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that
  can happen.
• Add --buildversion option, for tracking which version of a gene build was used. This is used
  during bcbio_setup_genome.py. Suggested formats are source_version, so Ensembl_94,
  EnsemblMetazoa_25, FlyBase_26, etc.
• Sort MACS2 bedgraph files before compressing. Thanks to @LMannarino for the suggestion.
• Check for the reserved field sample in RNA-seq metadata and quit with a useful error message.
  Thanks to @marypiper for suggesting this.
• Split ATAC-seq BAM files into nucleosome-free and mono/di/tri nucleosome files, so we can call
  peaks on them separately.
• Call peaks on NF/MN/DN/TN regions separately for each caller during ATAC-seq.
• Allow viral contamination to be assasyed on non tumor/normal samples.
• Ensure EBV coverage is calculated when run on genomes with it included as a contig.