├── .gitignore ├── .readthedocs.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── Thumbs.db ├── api.rst ├── benchmark.rst ├── conf.py ├── cplx_1.svg ├── cplx_2.svg ├── dna.svg ├── equal_alignment.svg ├── equal_variants.svg ├── examples.rst ├── index.rst ├── intro.rst ├── make.bat ├── mnv.svg ├── nf1.svg ├── pileup.svg ├── reads.svg ├── resource_usage.png ├── rna.svg └── snv_mnv.rst ├── indelpost ├── __init__.py ├── alleles.py ├── consensus.py ├── contig.pxd ├── contig.pyx ├── gappedaln.pyx ├── local_reference.pxd ├── local_reference.pyx ├── localn.pyx ├── pileup.pxd ├── pileup.pyx ├── softclip.pyx ├── sse2neon.h ├── ssw.c ├── ssw.h ├── sswpy.pyx ├── utilities.pxd ├── utilities.pyx ├── varaln.pxd ├── varaln.pyx ├── variant.pxd ├── variant.pyx └── version.py ├── pyproject.toml ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 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