├── .gitignore ├── .readthedocs.yaml ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── chain_files ├── .DS_Store ├── human │ ├── GRCh37_to_GRCh38.chain.gz │ ├── GRCh37_to_NCBI34.chain.gz │ ├── GRCh37_to_NCBI35.chain.gz │ ├── GRCh37_to_NCBI36.chain.gz │ ├── GRCh38_to_GRCh37.chain.gz │ ├── GRCh38_to_NCBI34.chain.gz │ ├── GRCh38_to_NCBI35.chain.gz │ ├── GRCh38_to_NCBI36.chain.gz │ ├── NCBI34_to_GRCh37.chain.gz │ ├── NCBI34_to_GRCh38.chain.gz │ ├── NCBI35_to_GRCh37.chain.gz │ ├── NCBI35_to_GRCh38.chain.gz │ ├── NCBI36_to_GRCh37.chain.gz │ └── NCBI36_to_GRCh38.chain.gz ├── mouse │ ├── GRCm38_to_NCBIM36.chain.gz │ ├── GRCm38_to_NCBIM37.chain.gz │ ├── NCBIM36_to_GRCm38.chain.gz │ └── NCBIM37_to_GRCm38.chain.gz └── readme.txt ├── docs ├── .DS_Store ├── Makefile ├── _build │ ├── .DS_Store │ ├── doctrees │ │ ├── environment.pickle │ │ └── index.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── CrossMap_vs_UCSC.png │ │ ├── howitworks.png │ │ └── logo.png │ │ ├── _sources │ │ └── index.rst.txt │ │ ├── _static │ │ ├── CrossMap_vs_UCSC.png │ │ ├── basic.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── howitworks.png │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── logo.png │ │ ├── mayo.jpg │ │ ├── mdacc.jpg │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ └── sourceforge.jpg │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── search.html │ │ └── searchindex.js ├── _static │ ├── .DS_Store │ ├── CrossMap_vs_UCSC.png │ ├── howitworks.png │ ├── logo.png │ ├── mayo.jpg │ ├── mdacc.jpg │ └── sourceforge.jpg ├── conf.py ├── crossMap_logo.png ├── index.rst ├── make.bat └── requirements.txt ├── pyproject.toml ├── setup.py └── src ├── CrossMap.egg-info ├── SOURCES.txt ├── dependency_links.txt ├── entry_points.txt ├── requires.txt └── top_level.txt ├── __init__.py └── cmmodule ├── BED.py ├── __init__.py ├── __pycache__ ├── BED.cpython-310.pyc ├── BED.cpython-312.pyc ├── BED.cpython-36.pyc ├── BED.cpython-37.pyc ├── BED.cpython-38.pyc ├── __init__.cpython-310.pyc ├── __init__.cpython-312.pyc ├── __init__.cpython-36.pyc ├── __init__.cpython-37.pyc ├── __init__.cpython-38.pyc ├── annoGene.cpython-310.pyc ├── annoGene.cpython-312.pyc ├── annoGene.cpython-36.pyc ├── annoGene.cpython-37.pyc ├── annoGene.cpython-38.pyc ├── bam_cigar.cpython-36.pyc ├── bgrMerge.cpython-310.pyc ├── bgrMerge.cpython-312.pyc ├── bgrMerge.cpython-36.pyc ├── bgrMerge.cpython-37.pyc ├── bgrMerge.cpython-38.pyc ├── fasta.cpython-36.pyc ├── fasta.cpython-37.pyc ├── fasta.cpython-38.pyc ├── helpinfo.cpython-38.pyc ├── ireader.cpython-310.pyc ├── ireader.cpython-312.pyc ├── ireader.cpython-36.pyc ├── ireader.cpython-37.pyc ├── ireader.cpython-38.pyc ├── mapbam.cpython-310.pyc ├── mapbam.cpython-312.pyc ├── mapbam.cpython-37.pyc ├── mapbam.cpython-38.pyc ├── mapbed.cpython-310.pyc ├── mapbed.cpython-312.pyc ├── mapbed.cpython-37.pyc ├── mapbed.cpython-38.pyc ├── mapgff.cpython-310.pyc ├── mapgff.cpython-312.pyc ├── mapgff.cpython-37.pyc ├── mapgff.cpython-38.pyc ├── mapgvcf.cpython-310.pyc ├── mapgvcf.cpython-312.pyc ├── mapgvcf.cpython-37.pyc ├── mapgvcf.cpython-38.pyc ├── mapmaf.cpython-310.pyc ├── mapmaf.cpython-312.pyc ├── mapmaf.cpython-37.pyc ├── mapmaf.cpython-38.pyc ├── mapregion.cpython-310.pyc ├── mapregion.cpython-312.pyc ├── mapregion.cpython-37.pyc ├── mapregion.cpython-38.pyc ├── mapvcf.cpython-310.pyc ├── mapvcf.cpython-312.pyc ├── mapvcf.cpython-37.pyc ├── mapvcf.cpython-38.pyc ├── mapwig.cpython-310.pyc ├── mapwig.cpython-312.pyc ├── mapwig.cpython-37.pyc ├── mapwig.cpython-38.pyc ├── meta_data.cpython-310.pyc ├── meta_data.cpython-312.pyc ├── meta_data.cpython-37.pyc ├── meta_data.cpython-38.pyc ├── myutils.cpython-310.pyc ├── myutils.cpython-312.pyc ├── myutils.cpython-36.pyc ├── myutils.cpython-37.pyc ├── myutils.cpython-38.pyc ├── sam_header.cpython-310.pyc ├── sam_header.cpython-312.pyc ├── sam_header.cpython-36.pyc ├── sam_header.cpython-37.pyc ├── sam_header.cpython-38.pyc ├── utils.cpython-310.pyc ├── utils.cpython-312.pyc ├── utils.cpython-37.pyc ├── utils.cpython-38.pyc ├── wig_reader.cpython-310.pyc ├── wig_reader.cpython-312.pyc ├── wig_reader.cpython-36.pyc ├── wig_reader.cpython-37.pyc └── wig_reader.cpython-38.pyc ├── annoGene.py ├── bgrMerge.py ├── ireader.py ├── mapbam.py ├── mapbed.py ├── mapgff.py ├── mapgvcf.py ├── mapmaf.py ├── mapregion.py ├── mapvcf.py ├── mapwig.py ├── meta_data.py ├── myutils.py ├── sam_header.py ├── utils.py ├── wig_reader.py └── wiggle.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liguowang/CrossMap/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liguowang/CrossMap/HEAD/.readthedocs.yaml 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