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>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
               d-shlibs,
               yaggo,
               pkg-config,
               bc,
               time,
               procps,
               swig,
               python3-all-dev,
               dh-python,
               perl,
               chrpath,
               libhts-dev,
               dos2unix,
               samtools
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Homepage: https://www.cbcb.umd.edu/software/jellyfish/
Rules-Requires-Root: no

Package: jellyfish
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Depends: ${shlibs:Depends},
         ${misc:Depends},
         libjellyfish-2.0-2 (= ${binary:Version})
Breaks: jellyfish-examples (<< 2.3.0-7)
Replaces: jellyfish-examples (<< 2.3.0-7)
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
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
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: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Multi-Arch: same
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: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
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: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
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
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
