Recursive config file traversal to expand all shell variables
Provide metadata target to specify sample sex and use to refine ploidy and final reported sex chromosomes. Correctly handles mitochondrial as well as X, Y. Fixes #33
Added file transaction to cutadapt.
Merge pull request #161 from mariogiov/recursive_shell_expansion

Recursive config file traversal to expand all shell variables
Explicitly update configuration when recursively setting paths; avoid relying on implicit dictionary updates #161
Remove mapping quality flag for FreeBayes. This is taken into account by default in recent versions: http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/#comment-1495