Ion Variant Hunter README
Feb. 2012
v. 0.1.2

**** BRIEF DESCRIPTION ****
Ion Variant Hunter is a unified variant caller, that uses flow intensities and alignments based
on bases and base counts (aka flowgram).

Variant Hunter produces both SNPs and InDels, but note that the Torrent Server variant
caller plugin only uses the InDel calls from this software.

**** SBCL INSTALLATION ****
For building the lisp component (ion-variant-hunter-core):
Requires sbcl to be installed.  Specific sbcl version used for TS 2.0.x was sbcl-1.0.51.

As a convenience only, internal Ion Torrent users can grab that sbcl binary compiled so that it will work
under both Ubuntu and CentOS 5.6 in the internal svn repo here:
svn/SWTEAM/trunk/eftsung/external/sbcl-binary-w-mods/sbcl-1.0.51.2x-backend-parms.binary.tgz
and follow the directions found in the README file.

What I did to produce this is to take the modifications to sbcl found in this package and compiled it
following instructions found in sbcl's README.  I did the compiling under CentOS 5.6 and the resulting binary
worked in Ubuntu. Note, compling under Ubuntu produces a binary that doesn't work under CentOS.

Modifications to sbcl used while building can be found in this package at
public/lisp/sbcl-mod/

For development, one can use slime with emacs. Both are available packages in Ubuntu 10.04.

**** JAVA Component ****
For the java component (SamToFlowSpace.jar):
Download sam-1.57.jar and picard-1.57.jar and place them in a folder
called lib (http://sourceforge.net/projects/picard/files/picard-tools/1.57/picard-tools-1.57.zip/download).


**** Building, cleaning, and running ****
To build:
ant

To clean:
ant clean

To run:
See RUNNING