├── .gitignore ├── .travis.yml ├── LICENSE ├── Makefile ├── README.md ├── advntr ├── __init__.py ├── __main__.py ├── acgt_filter.py ├── advntr_commands.py ├── coverage_bias.py ├── deep_recruitment.py ├── distance.py ├── genome_analyzer.py ├── hierarchical_clustering.py ├── hmm_utils.py ├── models.py ├── pacbio_haplotyper.py ├── pairwise_aln_generator.py ├── pattern_clustering.py ├── plot.py ├── profile_hmm.py ├── profiler.py ├── reference_editor.py ├── reference_vntr.py ├── sam_utils.py ├── settings.py ├── utils.py ├── vntr_annotation.py ├── vntr_finder.py └── vntr_graph.py ├── docs ├── Makefile ├── _build │ ├── .buildinfo │ ├── .doctrees │ │ ├── environment.pickle │ │ └── index.doctree │ ├── _sources │ │ └── index.txt │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── search.html │ └── searchindex.js ├── conf.py ├── description.rst ├── faq.rst ├── index.html ├── index.rst ├── installation.rst ├── make.bat ├── publication.rst ├── quickstart.rst └── tutorial.rst ├── filtering ├── README.md └── main.cc ├── pomegranate ├── __init__.py ├── base.pxd ├── base.pyx ├── distributions.pxd ├── distributions.pyx ├── hmm.pyx ├── utils.pxd └── utils.pyx ├── requirements-linux.txt ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── data └── hmm_utils.json ├── test_frameshift_identification.py ├── test_genotyping.py └── test_hmm_utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mehrdadbakhtiari/adVNTR/HEAD/.gitignore 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