The megSAP src folder contains the following sub-folders:
This folder contains the main anaylsis pipelines.
This folder contains common functionaity used by many script, e.g. for file and database handling. To include all functionality use 'all.php', it includes all other files.
This folder contains scripts that are used during installation only.
This folder contains scripts that are used in pipelines or other scripts, e.g. wrappers for BWA, freebayes, etc.
This folder contains auxilary scripts that are not part of the pipeline.
They are mainly used by the developers in Tübingen.
This folder contains scripts that are used by the developers in Tübingen only.
This folcer contains deprecated scrips that will be removed in the next release unless we get feedback that they are still needed.