Source: yanosim
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Nilesh Patra <nilesh@debian.org>
Build-Depends: debhelper-compat (= 13),
               python3,
               dh-python,
               python3-setuptools,
# make sure python3-pysam is avaliable on all architectures to enable testing migration
               python3-pysam
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/yanosim
Vcs-Git: https://salsa.debian.org/med-team/yanosim.git
Homepage: https://github.com/bartongroup/yanosim
Rules-Requires-Root: no
Testsuite: autopkgtest-pkg-python

Package: yanosim
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python3:Depends},
         python3-numpy,
         python3-scipy,
         python3-click,
         python3-pysam
Description: read simulator nanopore DRS datasets
 Yanosim has three options:
 .
 1. yanosim model:
    Creates an model of mismatches, insertions and deletions
    based on an alignment of nanopore DRS reads to a
    reference. Reads should be aligned to a transcriptome
    i.e. without spliced alignment, using minimap2. They
    should have the cs tag.
 2. yanosim quantify:
    Quantify the number of reads mapping to each
    transcript in a reference, so that the right number
    of reads can be simulated.
 3. yanosim simulate:
    Given a model created using yanosim model, and
    per-transcript read counts created using yanosim
    simulate, simulate error-prone long-reads from the
    given fasta file.