Consistently keep annotations and genotype information for split MNPs from vcfallelicprimitives. Thanks to @parlar
Merge pull request #655 from lpantano/upstream

add paired fastq files support and some extra docs
Handle zero division errors for FreeBayes calls with no read support. Fixes #656
Provide streaming of gzipped files from S3 with boto, allowing S3 fastqs as inputs to processing
Enable download of supporting files from S3 in configuration file
Provide additional normalize and duplicate removal for FreeBayes calls. Handle new grabix indexes. chapmanb/bcbio.variation#20
Always make a sequence index when setting up a custom genome.
Bump CNVkit to 0.2.4 to support small test examples
Identify WHAM output variants using classifier
Cleanly support gziped BED file inputs in configuration, which helps support retrieving these directly from S3
Improve S3 upload from bcbio. Ensure directory output is properly transferred and enable prefixing by folder to store within existing buckets
Simplify logic around post-processing to avoid race conditions when moving files. Thanks to @mjafin. #642
Fixes to S3 support to enable use via bcbio-vm
fix sample_name in csv when there are paired samples