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README.md

ILP for the Copy-Number Tree (CNT) Problem

============================================

License

Dependencies

Compilation instructions

To compile CNT, execute the following commands from the root of the repository:

mkdir build
cd build
cmake ..
make

Note: On Mac OS >= 10.9, you have to ensure that LEMON is linked against the old C++ standard library by editing LEMON's CMakeLists.txt file as follows.

if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
  set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
endif()

Also, if you are using CPLEX < 12.7 you must uncomment the same lines in the CMakeLists.txt of this repository. Instead, with the most recent versions of CPLEX >= 12.7, you can keep it as it is. In case CMake fails to detect either CPLEX or LEMON, run the following command with adjusted paths:

cmake \
-DLIBLEMON_ROOT=~/lemon \
-DCPLEX_INC_DIR=~/ILOG/cplex/include/ \
-DCPLEX_LIB_DIR=~/ILOG/cplex/lib/x86-64_osx/static_pic \
-DCONCERT_LIB_DIR=~/ILOG/concert/lib/x86-64_osx/static_pic \
-DCONCERT_INC_DIR=~/ILOG/concert/include/ ..

The compilation results in the following files in build directory:

  • cnt
  • visualize

Usage instructions

Input format

Example:

#PARAMS
1 #number of chromosomes
4 #number of leaves
10 #number of segments for each chromosome
#PROFILES
3 : 2 2 3 3 3 3 3 3 2 2
4 : 2 2 2 2 3 3 2 2 3 2
5 : 1 1 1 1 2 2 1 1 1 1
6 : 2 2 2 3 4 4 3 3 3 3

The first line must be #PARAMS. The three subsequent lines indicate the number of chromosomes, the number k of leaves and the number of segments for each chromosome (separated by a space). The fourth line must be #PROFILES. Then for each leaf the copy number profile is given (separated by spaces). It is recommended to label the leaves by the numbers k-1, ..., 2k-2.

Example executions

To run cnt:

./cnt -s 2 ../data/20160430/simC_c1_k4_n10_u1_s1_del02.input > result.txt

To visualize the resulting copy-number tree:

./visualize result.txt > T.dot
dot -Tpdf T.dot -o T.pdf

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Integer Linear Program for the Copy-Number Tree Problem

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