# Written by configureHomer.pl -make (cpp/Makefile)
cpp/*.o
cpp/analyzeHiC
cpp/assignGenomeAnnotation
cpp/compareMotifMatrices
cpp/findPeaks
cpp/findTADsAndLoopsFromRelMatrix
cpp/genomeOntology
cpp/getDifferentialPeaks
cpp/getGenomeTilingPeaks
cpp/getMappableRegions
cpp/getPeakTags
cpp/homer
cpp/homer2
cpp/homerTools
cpp/makeTagDirectory
cpp/makeUCSCfile
cpp/mergePeaks
bin/analyzeHiC
bin/assignGenomeAnnotation
bin/compareMotifMatrices
bin/findPeaks
bin/findTADsAndLoopsFromRelMatrix
bin/genomeOntology
bin/getDifferentialPeaks
bin/getGenomeTilingPeaks
bin/getMappableRegions
bin/getPeakTags
bin/homer
bin/homer2
bin/homerTools
bin/makeTagDirectory
bin/makeUCSCfile
bin/mergePeaks

# Written by hand after configuring; HOMER's scripts stop without it
/config.txt

__pycache__/
.pytest_cache/

# Written into the tree a benchmark builds
.paired-cache/
.bench-built

# Python packaging
/dist/
/build/
*.egg-info/
.ipynb_checkpoints/
