Merge branch 'mutect_version_check'
Finialize parallel alignment of bgzipped/grabix indexed fastq files. Only currently supported for bwa mem piped alignment. Handles mapping of regions and merging back into ready to process final BAM file
Avoid file naming errors for sample descriptions with periods. Fixes #123
Ensure parallel setup for split alignment has maximum core usage. Use parallel blocked gzip if available
Initial implementation of BAM to bgzip/grabix fastq for parallel alignment. Needs additional work to incorporate parallel bgzip
Remove old fastq split code, no longer used with grabix indexing that avoids IO/disk space penalties
Support split alignments for novoalign mapping
Avoid problematic psutil dependency which causes issues on CentOS #126
Adjust bwa mem/aln read size threshold based on latest man page recommendations
New approach for BAM to bgzipped FASTQ using biobambam to handling BAM to fastq conversion. Attempts to work around issues with streaming BAM to fastq
Enable additional memory to bamtofastq transfer. Check for errors due to truncated BAM input files
Provide installation and upgrade target --isolate to avoid updating PATH. Helps enable isolated environment installs. Fixes #125
Make sure to check that a summary exists before using it

Failing to check for this caused errors when write_summary was set to false.
Merge pull request #128 from porterjamesj/patch-1

Make sure to check that a summary exists before using it
Add paired tumor/normal calling to the pipeline documentation

Fixes issue #108
Merge pull request #130 from lbeltrame/doc-add-paired

Add paired tumor/normal calling to the pipeline documentation
Template for tumor/normal variant calling
Change specification of SGE/SLURM specific resources to use multiple arguments instead of munging together with semicolon. Avoids need to quote arguments on command line. Thanks to @mjafin
Merge pull request #132 from lbeltrame/paired-template

Template for tumor/normal variant calling
Rework ensemble calling to handle batch level calling. Default to new ensemble infrastructure in bcbio.variation.