sanger-pathogens/vr-codebase — pull request #154 by CraigPorter (2012-11-12 14:16:04+00:00)
Title: vrtracking_tool - mapped and snp_called

Vrtracking tool removes pathogens files when resetting snp_called.

Vrtracking tool resets mapped flag, deletes mapped entries in the mapstats table and removes files from disk.

Note: File deletion set to remove symlinks to nonexistent files - the -e test returns false for broken symlinks and we break the symlinks when deleting mapping files from the 'mapped' stage.