Source: python-varcode
Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Steffen Moeller <moeller@debian.org>,
Section: science
Testsuite: autopkgtest-pkg-pybuild
Build-Depends:
 debhelper-compat (= 14),
 dh-sequence-python3,
 pybuild-plugin-pyproject,
 pyensembl <!nocheck>,
 python3-all,
 python3-memoized-property <!nocheck>,
 python3-numpy <!nocheck>,
 python3-pandas <!nocheck>,
 python3-pysam <!nocheck>,
 python3-pytest <!nocheck>,
 python3-sercol (>= 1.0.3) <!nocheck>,
 python3-serializable (>= 1.1.0) <!nocheck>,
 python3-setuptools,
 python3-typechecks <!nocheck>,
Vcs-Browser: https://salsa.debian.org/med-team/python-varcode
Vcs-Git: https://salsa.debian.org/med-team/python-varcode.git
Homepage: https://github.com/openvax/varcode

Package: python3-varcode
Architecture: all
Section: python
Depends:
 python3-sercol (>= 1.0.3),
 python3-serializable (>= 1.1.0),
 python3-typechecks,
 ${python3:Depends},
Recommends:
 varcode (= ${source:Version}),
Suggests:
 python3-pysam,
Description: genomic variant effect prediction library for Python 3
 Varcode predicts how genomic variants affect genes, transcripts and proteins
 using Ensembl annotations. It handles single-nucleotide variants, insertions,
 deletions, multi-nucleotide substitutions and structural variants, and models
 their coding, splicing and protein-sequence consequences.
 .
 This package provides the Python 3 module. The command-line programs are
 available in the varcode package.

Package: varcode
Architecture: all
Depends:
 python3-varcode (= ${source:Version}),
 ${python3:Depends},
Description: command-line genomic variant effect prediction tools
 This package provides command-line interfaces to the Varcode library. The
 varcode command reads variants from VCF, MAF and JSON files, or accepts
 genomic coordinates directly, then reports overlapping genes and predicted
 effects on transcripts and protein sequences.
 .
 The varcode-genes command reports overlapping genes. The "varcode
 check-samples" command compares pairs of VCF samples by germline genotype
 concordance and shared somatic variants to flag possible sample mix-ups.