Source: maffilter
Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:
 Andreas Tille <tille@debian.org>,
 Julien Dutheil <julien.dutheil@univ-montp2.fr>,
 Pranav Ballaney <ballaneypranav@gmail.com>,
Section: science
Priority: optional
Build-Depends:
 debhelper-compat (= 13),
 cmake,
 texinfo,
 libbpp-phyl-omics-dev,
 libboost-iostreams-dev,
 zlib1g-dev,
 libbz2-dev,
Vcs-Browser: https://salsa.debian.org/med-team/maffilter
Vcs-Git: https://salsa.debian.org/med-team/maffilter.git
Homepage: https://jydu.github.io/maffilter/
Rules-Requires-Root: no

Package: maffilter
Architecture: any
Depends:
 ${shlibs:Depends},
 ${misc:Depends},
Suggests:
 maffilter-examples,
Description: process genome alignment in the Multiple Alignment Format
 MafFilter applies a series of "filters" to a MAF file, in order to
 clean it, extract data and computer statistics while keeping track of
 the associated meta-data such as genome coordinates and quality scores.
 .
  * It can process the alignment to remove low-quality / ambiguous /
    masked regions.
  * It can export data into a single or multiple alignment file in
    format such as Fasta or Clustal.
  * It can read annotation data in GFF or GTF format, and extract the
    corresponding alignment.
  * It can perform sliding windows calculations.
  * It can reconstruct phylogeny/genealogy along the genome alignment.
  * It can compute population genetics statistics, such as site
    frequency spectrum, number of fixed/polymorphic sites, etc.

Package: maffilter-examples
Architecture: all
Multi-Arch: foreign
Depends:
 ${misc:Depends},
Enhances:
 maffilter,
Description: process genome alignment in the Multiple Alignment Format (example data)
 MafFilter applies a series of "filters" to a MAF file, in order to
 clean it, extract data and computer statistics while keeping track of
 the associated meta-data such as genome coordinates and quality scores.
 .
  * It can process the alignment to remove low-quality / ambiguous /
    masked regions.
  * It can export data into a single or multiple alignment file in
    format such as Fasta or Clustal.
  * It can read annotation data in GFF or GTF format, and extract the
    corresponding alignment.
  * It can perform sliding windows calculations.
  * It can reconstruct phylogeny/genealogy along the genome alignment.
  * It can compute population genetics statistics, such as site
    frequency spectrum, number of fixed/polymorphic sites, etc.
 .
 This package provides example data for maffilter.
