hifimap

Hifimap is a mapping tool optimized for HiFi reads. Please see the original paper /hifimap_paper.pdf for more details.

Usage

To build hifimap run the following commands:

git clone https://github.com/staverm/hifimap && cd hifimap && mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release .. && make

which will create hifimap library, executable and unit tests.

Running make install will install the executable. In order to install the library, both biosoup and thread_pool (see Dependencies) need to be installed beforehand, and option hifimap_install used while configuring the build. Once the library is installed, a package will be copied to your system that can be searched and linked with:

find_package(hifimap)
target_link_libraries(<target> hifimap::hifimap)

Build options

• hifimap_install: generate library install target
• hifimap_build_exe: build executable
• hifimap_build_tests: build unit tests

Dependencies

• gcc 4.8+ | clang 3.5+
• cmake 3.11+
• pthread
• (hifimap_exe)(hifimap_test) zlib 1.2.8+

Hidden

• rvaser/biosoup 0.10.0
• rvaser/thread_pool 3.0.3
• (hifimap_exe)(hifimap_test) rvaser/bioparser 3.0.13
• (hifimap_test) google/googletest 1.10.0