CMakeLists.txt

README.md

cmake/SimpleTest.cmake

current_version.txt

doc/source/conf.py

doc/steps_to_prepare_release.md

docker/Dockerfile

docker/build_test.sh

include/AlevinHash.hpp

include/AlevinOpts.hpp

include/AlevinUtils.hpp

include/BarcodeModel.hpp

include/CollapsedCellOptimizer.hpp

include/DedupUMI.hpp

include/Filter.hpp

include/GZipWriter.hpp

include/ReadExperiment.hpp

include/SalmonConfig.hpp

include/SalmonDefaults.hpp

include/SalmonIndex.hpp