Source: jellyfish
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman@debian.org>,
           Andreas Tille <tille@debian.org>,
           Michael R. Crusoe <crusoe@debian.org>,
           Étienne Mollier <emollier@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
               architecture-is-little-endian,
               architecture-is-64-bit,
               d-shlibs,
               autoconf-archive,
               yaggo,
               pkgconf,
               bc,
               time,
               procps,
               swig,
               python3-all-dev:native,
               libpython3-all-dev,
               dh-sequence-python3,
               python3-setuptools,
               perl-xs-dev,
               perl:native,
               chrpath,
               libhts-dev,
               dos2unix,
               samtools
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Homepage: https://www.genome.umd.edu/jellyfish.html

Package: jellyfish
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         libjellyfish-2.0-2 (= ${binary:Version})
Description: count k-mers in DNA sequences
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.

Package: libjellyfish-2.0-2
Provides: libjellfish-2.0-2t64 (= ${binary:Version})
Replaces: libjellyfish-2.0-2t64
Conflicts: libjellyfish-2.0-2t64
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
         ${misc:Depends}
Description: count k-mers in DNA sequences (dynamic library of jellyfish)
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.
 .
 This package contains the dynamic library the main executable of
 jellyfish is linked to.

Package: libjellyfish-2.0-dev
Architecture: any
Section: libdevel
Depends: ${misc:Depends},
         libjellyfish-2.0-2 (= ${binary:Version})
Description: count k-mers in DNA sequences (development files of jellyfish)
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.
 .
 This package contains the development files (static library and
 header files)

Package: python3-dna-jellyfish
Architecture: any
Section: python
Depends: ${python3:Depends},
         ${misc:Depends},
         ${shlibs:Depends}
Description: count k-mers in DNA sequences (Python bindings of jellyfish)
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.
 .
 This package contains the Python bindings of jellyfish.

Package: libjellyfish-perl
Architecture: any
Multi-Arch: same
Section: perl
Depends: ${perl:Depends},
         ${misc:Depends},
         ${shlibs:Depends}
Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.
 .
 This package contains the Perl bindings of jellyfish.

Package: jellyfish-examples
Architecture: all
Multi-Arch: foreign
Depends: ${shlibs:Depends},
         ${misc:Depends}
Recommends: jellyfish
Description: count k-mers in DNA sequences (examples for testing)
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the "compare-and-swap" CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the "jellyfish dump" command.
 .
 This package contains examples to test the package
