Makefile

README.md

docs/conf.py

docs/index.rst

src/nucBed/nucBed.cpp

src/shuffleBed/shuffleBed.cpp

src/shuffleBed/shuffleBedMain.cpp

src/utils/bedFile/bedFile.cpp

src/utils/bedFile/bedFile.h

src/utils/fileType/fileType.cpp

test/general/test-general.sh

test/map/test-map.sh

test/reldist/test-reldist.sh

test/shuffle/excl.bed

test/shuffle/incl.bed

test/shuffle/simrep.bed

test/shuffle/test-shuffle.sh

test/test.sh