Trim two lanes of a paired lane in parallel.
Work towards improved distributed logging for local, multiprocessing and ipython/ZeroMQ cases
Improved logging: debug for single and multicore runs. Stream process standard out and error to debug log file for quick asssessment of progress and debugging
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Fix for grabbing the URI for the logbook zmq handler.
Distributed logging fixes for ZeroMQ. Add Logbook handlers that merge multiple logging streams into a single log. Fix for multiprocessing logging within ipython processes. Log running commandlines to a single file
Merge with Rory's changes
Shift debug level output to debug specific logging file to limit information in top level log
Ensure closing of subprocess stdout and stderr pipes, avoiding errors due to too many open files
make sure target file exists.
Merge pull request #21 from brentp/check-target

make sure target file exists.
Enable alignment post-preparation with recalibration and no de-duplication, supporting pre-duplicated inputs. Thanks to @brentp
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Handle GATK BAM preparation with recalibration on genome regions without aligned reads
Improve documentation on difference between hybrid_regions and variant_regions
More robust naming of ID and SM read group information to avoid downstream conflicts. Add upstream checks at configuration read time to identify issues. Move naming and preparation checking to single location. Thanks to Zhengqiu Cai for problem report
Reduce default for number of split regions until IPython file handle issue is resolved
Work around VarScan issue where it failes to generate a VCF header on regions that start with zero coverage. Thanks to @brentp for problem report
Avoid installation problem with ipython and git submodules by using editable flag. Fixes #23
Explicitly clean up ZeroMQ logging handlers used in IPython tasks, avoiding leaving open TCP connections. Fixes issues with large job numbers so revert regional splitting back to previous defaults