├── .gitattributes ├── .gitignore ├── .travis.yml ├── Dockerfile ├── LICENSE ├── README.md ├── README.txt ├── example_usage.ipynb ├── paper.bib ├── paper.md ├── schematic.jpg ├── setup.py └── xenomapper ├── __init__.py ├── mappability.py ├── tests ├── __init__.py ├── data │ ├── paired_end_testdata_human.bam │ ├── paired_end_testdata_human.sam │ ├── paired_end_testdata_mouse.bam │ ├── paired_end_testdata_mouse.sam │ ├── test_from_EcoliK12DH10B.1.bt2 │ ├── test_from_EcoliK12DH10B.2.bt2 │ ├── test_from_EcoliK12DH10B.3.bt2 │ ├── test_from_EcoliK12DH10B.4.bt2 │ ├── test_from_EcoliK12DH10B.fasta │ ├── test_from_EcoliK12DH10B.rev.1.bt2 │ ├── test_from_EcoliK12DH10B.rev.2.bt2 │ ├── test_from_EcoliK12DH10B_10reads.fasta │ ├── test_from_EcoliK12DH10B_10reads.sam │ ├── test_from_EcoliK12DH10B_10reads.wig │ ├── test_from_EcoliK12DH10B_150reads.fasta │ ├── test_from_EcoliK12DH10B_150reads.sam │ ├── test_from_EcoliK12DH10B_150reads.wig │ ├── test_human_in.sam │ └── test_mouse_in.sam ├── test_all.py 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