Add single sample calling to joint/pooled/single analysis. Add instructions for running to documentation
Check for problematic paired end inputs with only normal and non-tumor samples. Thanks to @mjafin
Swap ensembl yeast name to lowercase to make retrieval and cache preparation happy. Thanks to John Kern.
Add back in cleanup of VarScan lines to avoid ambiguous base calls not caught by awk script. #571"
Generalize transactional directory creation: rename, centralize and handle global directories called from multiple processes and machines. Support towards using local disk for all transactional processes
Unified approach for writing temporary transactional files that enables use of a global temporary directory. Supports bcbio on AWS with a shared filesystem
Support samtools 1.0 multiallelic calling
Normalize and split MNPs in samtools called variants