Merge pull request #24 from guillermo-carrasco/master

Sync bcbio-nextgen with @chapmanb
move code to pipeline/fastq.py and handle mix up of fastq/fastq.gz samples
Merge pull request #25 from guillermo-carrasco/master

Yes I want to keep doing this
change var names, and remove old code
Merge pull request #652 from lpantano/upstream

update prepare_samples
Ensure speedseq calls to lumpy python scripts use installed bcbio python with dependencies. Fixes #653
Swap S3 input/output to use gof3r with support for parallel upload/download.
fix kraken to use fastq or fastq.gz files

better coding style
Move dbNSFP download to 2.7 release. Thanks to Craig Bohrson
Merge pull request #654 from lpantano/upstream

some fixes for kraken tool
add paired fastq files  support

add documentation

support paired fastq files and add doc
fix typos
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