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qgenlib

Libraries for quantitative genomics

Overview

qgenlib is a collection of C++ libraries (and test binaries) to help quantitative genomic analysis.

Installing qgenlib

Before installing qgenlib, you need to install htslib in the same directory you want to install qgenlib' (i.e. qgenlibandhtslib` should be siblings directories). You also need cmake installed in your system.

After installing htslib, you can clone the current snapshot of this repository to install as well

$ mkdir build

$ cd build

$ cmake ..

In case any required libraries is missing, you may specify customized installing path by replacing "cmake .." with:

For libhts:
  - $ cmake -DHTS_INCLUDE_DIRS=/htslib_absolute_path/include/  -DHTS_LIBRARIES=/htslib_absolute_path/lib/libhts.a ..

For bzip2:
  - $ cmake -DBZIP2_INCLUDE_DIRS=/bzip2_absolute_path/include/ -DBZIP2_LIBRARIES=/bzip2_absolute_path/lib/libbz2.a ..

For lzma:
  - $ cmake -DLZMA_INCLUDE_DIRS=/lzma_absolute_path/include/ -DLZMA_LIBRARIES=/lzma_absolute_path/lib/liblzma.a ..

Finally, to build the binary, run

$ make

List of test applications contained in qgenlib

qgenlib contains many in-house C++ tools that are currently under the hood development phase. To list the available commands of tools, type:

testqgen --help

To see the usage of individual commands, type:

testqgen [command] --help