CMakeLists.txt
FindGUROBI.cmake
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
custom/GATK4-CNV/allelecn.png
custom/GATK4-CNV/cbb.png
custom/GATK4-CNV/custom-gatk4-cnv.sh
custom/GATK4-CNV/demo-gatk4-cnv.md
custom/GATK4-CNV/demo-gatk4-cnv.sh
custom/GATK4-CNV/gatk4cnsToBB.py
custom/GATK4-CNV/profiles.png
custom/GATK4-CNV/sample1.GATK4.CNV.seg
custom/GATK4-CNV/sample2.GATK4.CNV.seg
custom/GATK4-CNV/totalcn.png
custom/setup-preprocess/setup.md
custom/setup-preprocess/setup.sh
script/README.md
script/hatchet.ini
src/argparse.cpp
src/argparse.h
src/bbc_instance.cpp
src/bbc_instance.h
src/coordinate_descent.cpp
src/coordinate_descent.h
src/gurobi-utils.h
src/ilp-min.cpp
src/ilp-min.h
src/input_instance.cpp
src/input_instance.h
src/solve.cpp
src/utils.cpp
src/utils.h
src/worker.cpp
src/worker.h
src/hatchet/__init__.py
src/hatchet/__main__.py
src/hatchet/hatchet.ini
src/hatchet.egg-info/PKG-INFO
src/hatchet.egg-info/SOURCES.txt
src/hatchet.egg-info/dependency_links.txt
src/hatchet.egg-info/entry_points.txt
src/hatchet.egg-info/not-zip-safe
src/hatchet.egg-info/requires.txt
src/hatchet.egg-info/top_level.txt
src/hatchet/bin/HATCHet-preprocess.py
src/hatchet/bin/HATCHet.py
src/hatchet/bin/__init__.py
src/hatchet/data/__init__.py
src/hatchet/data/hg19.centromeres.txt
src/hatchet/data/hg38.centromeres.txt
src/hatchet/data/sample.bbc
src/hatchet/data/sample.seg
src/hatchet/data/sample.sorted.bam
src/hatchet/data/sample.sorted.gff.gz
src/hatchet/utils/ArgParsing.py
src/hatchet/utils/BAMBinning.py
src/hatchet/utils/CoordinateFinding.py
src/hatchet/utils/ProgressBar.py
src/hatchet/utils/Supporting.py
src/hatchet/utils/TotalCounting.py
src/hatchet/utils/__init__.py
src/hatchet/utils/check.py
src/hatchet/utils/check_solver.py
src/hatchet/utils/cluster_bins.py
src/hatchet/utils/cluster_bins_gmm.py
src/hatchet/utils/combine_counts.py
src/hatchet/utils/combine_counts_fw.py
src/hatchet/utils/commands.py
src/hatchet/utils/config.py
src/hatchet/utils/count_alleles.py
src/hatchet/utils/count_reads.py
src/hatchet/utils/count_reads_fw.py
src/hatchet/utils/download_panel.py
src/hatchet/utils/genotype_snps.py
src/hatchet/utils/multiprocessing.py
src/hatchet/utils/phase_snps.py
src/hatchet/utils/plot_bins.py
src/hatchet/utils/plot_bins_1d2d.py
src/hatchet/utils/plot_cn.py
src/hatchet/utils/plot_cn_1d2d.py
src/hatchet/utils/run.py
src/hatchet/utils/solve/__init__.py
src/hatchet/utils/solve/cd.py
src/hatchet/utils/solve/ilp_subset.py
src/hatchet/utils/solve/utils.py