Improved Bayesian inversion somatic caller
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build-common
cmake
debian
integration-test
perl
src
test/lib
vendor
version
CMakeLists.txt
PackageInfo.cmake
README
basovac.pl

README

==============================================================================
Compiling Bassovac
==============================================================================

------------------------------------------------------------------------------
1) Dependencies
------------------------------------------------------------------------------

The build process requires the following tools:
    CMake 2.8   (http://www.cmake.org)
    boost 1.40+ (http://www.boost.org)

If you are running a recent, debian based distro this may work for you:

    sudo apt-get install libboost-all-dev cmake

------------------------------------------------------------------------------
2) Setup build environment
------------------------------------------------------------------------------

First, make sure your checkout is complete by initializing the build-common
submodule:

    git submodule update --init build-common


Next, create an out-of-source build directory, change into it, and run cmake
with the path to the top of the bassovac checkout. For example, to build in a
subdirectory of the checkout called 'build', one runs:

    mkdir build
    cd build
    cmake ..

Or to build in /tmp:

    mkdir /tmp/build-bassovac
    cd /tmp/build-bassovac
    cmake ~/path/to/bassovac/checkout

------------------------------------------------------------------------------
3) Build and test
------------------------------------------------------------------------------

To build, simply run make in the build directory.  Once make is finished, you
can run the unit test suite by executing 'ctest' from the build directory. All
binaries can be found in the bin/ subdirectory where you built.


==============================================================================
Output Format
==============================================================================

The tab separated output fields are:

 1) sequence name (chromosome)
 2) start position 
 3) end position 
 4) reference base
 5) total normal reads at this position
 6) # normal reads supporting reference
 7) harmonic mean of normal base qualities
 8) total tumor reads at this position
 9) # tumor reads supporting reference
10) harmonic mean of tumor base qualities
11) probability of homozygous variant
12) probability of heterozygous variant
13) probability of somatic variant
14) probability of loss of heterozygosity event
15) probability of 'non-interesting' event