change sample temparory directory from names["sample"] to names["lane"]
fixed STAR juction input for oncofuse with GRCh37
disable tophat input for now
only works for GRCh37/hg19 genome
resume support for tophat-oncofuse
add checks to make sure the junction file exists before running oncofuse
upload oncofuse output to final directory
catch case where no fusion transcripts are loaded
put tophat2 as the default aligner
temporary solution
Modified bcbio/structural/cn_mops.py to accept regions rather than always using the whole chromosomes.
Removed debugging lines.
Generalize FreeBayes depth filter to handle multiple depths and qualities. Bump requirements to get new ipython-cluster-helper
Added a check for whether coverage_interval is genome to pass using a bed file
Update exome validation run to use latest GiaB reference and pre-prepped shell script for download
Correctly prepare VCF subset names when group or samples names are integers
Ensure gemini database creation uses available cores when run in parallel; no longer need to have explicit data argument with handling of sample lists in config_utils
Merge pull request #407 from tanglingfung/master

Oncofuse bug fixes.

This should be considered pre-alpha, we haven't been able to validate the calls but this should get us started.

Thanks to @tanglingfung for all of his awesome work.
Use STAR as the default test fusion aligner.

Update fusion tests as expected to pass.
Fixes for gemini parallelization: re-use previously created batch variation files. Handle ipython parallelization for gemini with nested configurations
Improvements for new split/combine/batch approach: reduce memory usage by using dictionary based diffs of nested groups. Collapse regional calls when not in use for parallelization. Ensure batching for population preparation works correctly with multiple callers
Merge pull request #415 from mjafin/cnmops

Cn.mops support bed files