Read Me

Parliament - 
	The tool for merging SV calls across multiple programs and data-sources.

   This README.txt contains information about how the Parliament is layed   	
   out as well as developer notes.
   
   Users should start with docs/INSTALL.txt for a guide on how to setup
   Parliament.
   Once everything is intalled, begin reading docs/Notes.txt for a guide on
   how to use Parliament.


Develper Notes

Parliament Directory Structure

   setup.sh  -  Bash script for setting your environment up everything Parliament needs.
   docs      -  Documentation on everything Parliament does and contains.
   src       -  Code base.
   misc      -  Various files that are useful (like annotations).
   bin       -  Executables including pipeline code that chains several src/ programs.
   packages  -  python packages and programs that Parliament needs (excluding pip installable).
   local     -  Working data for my local Parliament runs (HS1011). This SHOULD NOT be put in repository.

Another pip of scikit-learn==0.14.1
pip install scipy=0.13.3

TodoPriorties (1! to 5! lowest to highest priority)
TODO:

!!!!! Begin work on OrangeTable....
!!! Redo freeze2 so that JSO and JAR have SVPNames. 
!! Need a calls to .bed tool (split with names and stuff)
    Document SVPName somewhere or make SVPIO automatically populate names with
    abbrev and an ID (becareful with ResultSets and such.. maybe just
    Program.abbrev Result.rsid . Call.id
!! Need a script that will do all of the db creation and population all in one
! create a "make" file that does all of the setting up that I currently put on
  the user
   go (see docs/Notes "Here's how you will make the database")
! ReProcesssing instead of completely reloading?
! Document how to start svplims.py
!! Tabix Documentation		for i in ../*.bed; do python sortBed.py $i |
bgzip > temp.bed && tabix -p bed -0 temp.bed && mv temp.bed.tbi $i.tbi ; done
NOTES: