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Very fast and efficient detection of multiple overlaps between genomic regions. For details on the algorithm and the implementation, please refer to the following publication: Aszódi, A. (2012): MULTOVL: Fast multiple overlaps of genomic regions. Bioinformatics 28: 3318-3319.
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README.txt

MULTIPLE OVERLAP OF GENOMIC REGIONS
===================================

by Andras Aszodi
Version 1.3

See doc/html/guide.html for installation instructions
and a detailed documentation.

This program is licensed under the terms of the BSD Open Source license.
See the file LICENSE for details.

Pre-compiled binaries are provided for some popular architectures.
If you want to build Multovl from scratch, keep on reading:

Building Instructions for the Impatient
---------------------------------------

You will need cmake 2.8 or above, a C++98-compliant compiler, 
and the Boost libraries (1.44 or above) to build Multovl.

By default all these external libraries will be linked statically.
To link all of them dynamically instead, specify the CMake option
-DMULTOVL_USE_DYNAMIC_LIBS:BOOL=ON

The basic steps if you use the default system compilers:

mkdir build 
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DBOOST_ROOT=/path/to/boost \
    -DCMAKE_INSTALL_PREFIX=/path/to/installdir ..
make

Or you can spell out what make all does:

make apps
make doc    (this generates Doxygen documentation if you have Doxygen installed)

And then finally:

make install (this you may need to run as root, depending on installdir permissions)

The tools should now be installed in ${CMAKE_INSTALL_PREFIX}/multovl-1.3/bin.

Additional Cmake settings are listed in the top-level CMakeLists.txt, or you may run
cmake -i for interactive options, or ccmake.
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