.gitignore
CMakeLists.txt
LICENSE
README.md
README.rst
pyproject.toml
setup.py
.github/workflows/build_wheels.yml
.github/workflows/report-results.yml
debug/Dockerfile.cmake
debug/Dockerfile.yum
debug/build_image.sh
debug/build_wheel.sh
debug/debug_cibuildwheel.sh
epigeec/__init__.py
epigeec/_version.py
epigeec.egg-info/PKG-INFO
epigeec.egg-info/SOURCES.txt
epigeec.egg-info/dependency_links.txt
epigeec.egg-info/entry_points.txt
epigeec.egg-info/requires.txt
epigeec.egg-info/top_level.txt
epigeec/bin/.gitkeep
epigeec/cc/bg_to_hdf5/CMakeLists.txt
epigeec/cc/bg_to_hdf5/bg_to_hdf5.cc
epigeec/cc/bw_to_hdf5/CMakeLists.txt
epigeec/cc/bw_to_hdf5/bw_to_hdf5.cc
epigeec/cc/core/CMakeLists.txt
epigeec/cc/core/bed_reader.cc
epigeec/cc/core/bed_reader.h
epigeec/cc/core/bedgraph_reader.cc
epigeec/cc/core/bedgraph_reader.h
epigeec/cc/core/bigwig_reader.cc
epigeec/cc/core/bigwig_reader.h
epigeec/cc/core/chrom_size.cc
epigeec/cc/core/chrom_size.h
epigeec/cc/core/filter_bitset.cc
epigeec/cc/core/filter_bitset.h
epigeec/cc/core/genomic_data_line.cc
epigeec/cc/core/genomic_data_line.h
epigeec/cc/core/genomic_dataset.cc
epigeec/cc/core/genomic_dataset.h
epigeec/cc/core/genomic_file_reader.cc
epigeec/cc/core/genomic_file_reader.h
epigeec/cc/core/genomic_file_reader_factory.cc
epigeec/cc/core/genomic_file_reader_factory.h
epigeec/cc/core/hdf5_dataset.cc
epigeec/cc/core/hdf5_dataset.h
epigeec/cc/core/hdf5_dataset_factory.cc
epigeec/cc/core/hdf5_dataset_factory.h
epigeec/cc/core/hdf5_reader.cc
epigeec/cc/core/hdf5_reader.h
epigeec/cc/core/hdf5_writer.cc
epigeec/cc/core/hdf5_writer.h
epigeec/cc/core/input_list.cc
epigeec/cc/core/input_list.h
epigeec/cc/correlation/CMakeLists.txt
epigeec/cc/correlation/correlation.cc
epigeec/cc/correlation_nm/CMakeLists.txt
epigeec/cc/correlation_nm/correlation_nm.cc
epigeec/cc/correlation_w/CMakeLists.txt
epigeec/cc/correlation_w/correlation_w.cc
epigeec/cc/correlation_w_nm/CMakeLists.txt
epigeec/cc/correlation_w_nm/correlation_w_nm.cc
epigeec/cc/filter/CMakeLists.txt
epigeec/cc/filter/filter.cc
epigeec/lib/.gitkeep
epigeec/python/__init__.py
epigeec/python/core/__init__.py
epigeec/python/core/config.py
epigeec/python/core/error.py
epigeec/python/core/input_parser.py
epigeec/python/core/launcher.py
epigeec/python/core/main.py
epigeec/python/core/make_matrix.py
epigeec/python/core/utils.py
epigeec/python/core/validators.py
epigeec/resource/chrom_sizes/hg19.can.chrom.sizes
epigeec/resource/chrom_sizes/hg19.ext.chrom.sizes
epigeec/resource/chrom_sizes/hg19.noy.chrom.sizes
epigeec/resource/chrom_sizes/hg38.can.chrom.sizes
epigeec/resource/chrom_sizes/hg38.ext.chrom.sizes
epigeec/resource/chrom_sizes/hg38.noy.chrom.sizes
epigeec/resource/chrom_sizes/mm10.can.chrom.sizes
epigeec/resource/chrom_sizes/mm10.ext.chrom.sizes
epigeec/resource/chrom_sizes/mm10.noy.chrom.sizes
epigeec/resource/chrom_sizes/saccer3.can.chrom.sizes
epigeec/resource/filter/hg19.blklst.bed
epigeec/resource/filter/hg19.gene.bed
epigeec/resource/filter/hg19.tss.bed
epigeec/resource/filter/hg38.gene.bed
epigeec/resource/filter/hg38.tss.bed
epigeec/resource/filter/mm10.blklst.bed
epigeec/test/__init__.py
epigeec/test/error_test.py
epigeec/test/filter_test.py
epigeec/test/test.py
epigeec/test/utils_test.py
epigeec/test/files/expected
epigeec/test/files/expected_hg19
epigeec/test/files/expected_nm
epigeec/test/files/expected_w
epigeec/test/files/hdf5/test.hdf5
epigeec/test/files/signal/001f63cdf00286183e32c1bb0fd6d85f
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epigeec/test/reports/add_build_info_to_ctrf.py
epigeec/test/reports/ctrf-summary-template.hbs
third_party/bwreader/CMakeLists.txt
third_party/bwreader/include/bwreader/BBFileHeader.h
third_party/bwreader/include/bwreader/BBFileReader.h
third_party/bwreader/include/bwreader/BBTotalSummaryBlock.h
third_party/bwreader/include/bwreader/BBZoomLevelFormat.h
third_party/bwreader/include/bwreader/BBZoomLevelHeader.h
third_party/bwreader/include/bwreader/BBZoomLevels.h
third_party/bwreader/include/bwreader/BPTree.h
third_party/bwreader/include/bwreader/BPTreeChildNode.h
third_party/bwreader/include/bwreader/BPTreeChildNode.h (dinf-prospe-03b's conflicted copy 2013-08-14).cbTemp
third_party/bwreader/include/bwreader/BPTreeChildNodeItem.h
third_party/bwreader/include/bwreader/BPTreeHeader.h
third_party/bwreader/include/bwreader/BPTreeLeafNode.h
third_party/bwreader/include/bwreader/BPTreeLeafNodeItem.h
third_party/bwreader/include/bwreader/BPTreeNode.h
third_party/bwreader/include/bwreader/BPTreeNodeItem.h
third_party/bwreader/include/bwreader/BedFeature.h
third_party/bwreader/include/bwreader/BigBedDataBlock.h
third_party/bwreader/include/bwreader/BigBedIterator.h
third_party/bwreader/include/bwreader/BigWigDataBlock.h
third_party/bwreader/include/bwreader/BigWigIterator.h
third_party/bwreader/include/bwreader/BigWigSection.h
third_party/bwreader/include/bwreader/BigWigSectionHeader.h
third_party/bwreader/include/bwreader/BigWigSectionHelper.h
third_party/bwreader/include/bwreader/RPChromosomeRegion.h
third_party/bwreader/include/bwreader/RPTree.h
third_party/bwreader/include/bwreader/RPTreeChildNode.h
third_party/bwreader/include/bwreader/RPTreeChildNodeItem.h
third_party/bwreader/include/bwreader/RPTreeHeader.h
third_party/bwreader/include/bwreader/RPTreeLeafNode.h
third_party/bwreader/include/bwreader/RPTreeLeafNodeItem.h
third_party/bwreader/include/bwreader/RPTreeNode.h
third_party/bwreader/include/bwreader/RPTreeNodeItem.h
third_party/bwreader/include/bwreader/RPTreeNodeProxy.h
third_party/bwreader/include/bwreader/WigItem.h
third_party/bwreader/include/bwreader/ZoomDataBLoch.h
third_party/bwreader/include/bwreader/ZoomDataBlock.h
third_party/bwreader/include/bwreader/ZoomDataRecord.h
third_party/bwreader/include/bwreader/ZoomLevelIterator.h
third_party/bwreader/include/bwreader/decompress_util.h
third_party/bwreader/include/bwreader/endian_helper.h
third_party/bwreader/include/bwreader/enum_global.h
third_party/bwreader/include/bwreader/smart_pointer.h
third_party/bwreader/src/BBFileReader.cpp
third_party/bwreader/src/BBTotalSummaryBlock.cpp
third_party/bwreader/src/BBZoomLevelFormat.cpp
third_party/bwreader/src/BBZoomLevelHeader.cpp
third_party/bwreader/src/BBZoomLevels.cpp
third_party/bwreader/src/BPTree.cpp
third_party/bwreader/src/BPTreeChildNode.cpp
third_party/bwreader/src/BPTreeChildNode.h (dinf-prospe-03b's conflicted copy 2013-08-14).cbTemp
third_party/bwreader/src/BPTreeChildNodeItem.cpp
third_party/bwreader/src/BPTreeHeader.cpp
third_party/bwreader/src/BPTreeLeafNode.cpp
third_party/bwreader/src/BPTreeLeafNodeItem.cpp
third_party/bwreader/src/BigBedDataBlock.cpp
third_party/bwreader/src/BigBedIterator.cpp
third_party/bwreader/src/BigWigDataBlock.cpp
third_party/bwreader/src/BigWigIterator.cpp
third_party/bwreader/src/BigWigSection.cpp
third_party/bwreader/src/BigWigSectionHeader.cpp
third_party/bwreader/src/BigWigSectionHelper.cpp
third_party/bwreader/src/RPChromosomeRegion.cpp
third_party/bwreader/src/RPTree.cpp
third_party/bwreader/src/RPTreeChildNode.cpp
third_party/bwreader/src/RPTreeChildNodeItem.cpp
third_party/bwreader/src/RPTreeHeader.cpp
third_party/bwreader/src/RPTreeLeafNode.cpp
third_party/bwreader/src/RPTreeLeafNodeItem.cpp
third_party/bwreader/src/RPTreeNodeProxy.cpp
third_party/bwreader/src/ZoomDataRecord.cpp
third_party/bwreader/src/ZoomLevelIterator.cpp
third_party/bwreader/src/endian_helper.cpp