Add initial check for pdflatex, required for report generation. Fixes #114
Add new mm10 resource file with pointers to dbSNP resources, matching updated CloudBioLinux data. Bump mm10 resource version
Facilities to pre-index FASTQ input files witn bgzip and grabix. Initial steps towards parallelizing alignment over machines as well as nodes.
Avoid overwriting sudo argument from defaults when specified on command line
Improve python dependency installation: use latest pyzmq from binstar. Avoid duplication of dependencies by reading from requirements.txt in setup.py
Documentation for setting SGE parallel environment to use through resources flag
Generalize checking for bowtie references to avoid failing when non-bowtie files like FASTA references are present. Fixes #115
IPython parallelization improvements: handle ZeroMQ logging interrupts and avoid using local checkpoints when global IPython enabled
Fixes for new functionality to skip local checkpoints on global. Do not spin up initial cluster when align_split_size used since will be a non-immediate operation
Avoid expanding paths for algorithm variables that can match local work directories. Thanks to @brentp for report.
Provide checks for unexpectedly small alignment outputs which appear to occur due to silent errors in samtools sorting
Merge pull request #120 from mariogiov/mutect_version_check

Mutect version check
Merge pull request #121 from mariogiov/jar_versioner_info

Jar versioner info
Provide additional framework implementations for parallel alignment. Separate alignment and post processing and add hook to do post-split alignment merging
Roll back to older pyzmq until 13.1.0 packaging problems on CentOS resolved
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