Source: cnvkit
Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Michael R. Crusoe <crusoe@debian.org>,
 Steffen Moeller <moeller@debian.org>,
 Olivier Sallou <osallou@debian.org>,
Section: science
Testsuite: autopkgtest-pkg-pybuild
Build-Depends:
 debhelper-compat (= 13),
 dh-sequence-python3,
 python3,
 python3-setuptools,
 pybuild-plugin-pyproject,
 python3-pytest <!nocheck>,
 python3-pyfaidx (>> 0.8.1.3) <!nocheck>,
 python3-biopython (>> 1.85) <!nocheck>,
 python3-pandas (>> 2.2.3) <!nocheck>,
 python3-numpy <!nocheck>,
 python3-pysam (>> 0.23.0) <!nocheck>,
 python3-scipy (>> 1.14.1) <!nocheck>,
 python3-matplotlib (>> 3.9) <!nocheck>,
 python3-pomegranate (>= 1.0) <!nocheck>,
 r-bioc-dnacopy <!nocheck>,
# testing
# poppler-utils provides pdfunite, needed for the tests
 poppler-utils <!nocheck>,
Vcs-Browser: https://salsa.debian.org/med-team/cnvkit
Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git
Homepage: https://cnvkit.readthedocs.org
Rules-Requires-Root: no

Package: cnvkit
Architecture: all
Depends:
 ${python3:Depends},
 ${misc:Depends},
 r-bioc-dnacopy,
Description: Copy number variant detection from targeted DNA sequencing
 A command-line toolkit and Python library for detecting copy number variants
 and alterations genome-wide from targeted DNA sequencing. It is designed for
 use with hybrid capture, including both whole-exome and custom target panels,
 and short-read sequencing platforms such as Illumina and Ion Torrent.