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Source: libssw
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>,
Michael R. Crusoe <crusoe@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
default-jdk-headless <!nojava>,
javahelper <!nojava>,
help2man,
zlib1g-dev,
libsimde-dev,
maven-repo-helper <!nojava>
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libssw
Vcs-Git: https://salsa.debian.org/med-team/libssw.git
Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
Rules-Requires-Root: no
Package: libssw1
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
zlib1g
Pre-Depends: ${misc:Pre-Depends}
Description: fast SIMD parallelized implementation of the Smith-Waterman algorithm
SSW is a fast implementation of the Smith-Waterman algorithm, which uses the
Single-Instruction Multiple-Data (SIMD) instructions to parallelize the
algorithm at the instruction level. SSW library provides an API that can be
flexibly used by programs written in C, C++ and other languages. The library
can do protein and genome alignment directly.
Current version of this implementation is ~50 times faster than an ordinary
Smith-Waterman. It can return the Smith-Waterman score, alignment location
and traceback path (cigar) of the optimal alignment accurately; and return
the sub-optimal alignment score and location heuristically.
Package: libssw-dev
Architecture: any
Multi-Arch: same
Section: libdevel
Depends: ${misc:Depends},
libssw1 (= ${binary:Version})
Pre-Depends: ${misc:Pre-Depends}
Provides: libssw-dev
Description: Development headers and static libraries for libssw
This package provides development headers and static libraries for libssw,
a fast implementation of the Smith-Waterman algorithm using
Single-Instruction Multiple-Data (SIMD) instructions to parallelize the
algorithm at the instruction level.
Package: libssw-java
Build-Profiles: <!nojava>
Architecture: any
Section: java
Depends: ${java:Depends},
${shlibs:Depends},
${misc:Depends}
Recommends: ${java:Recommends}
Description: Java bindings for libssw
This package provides JNI based Java bindings for libssw, a fast
implementation of the Smith-Waterman algorithm using Single-Instruction
Multiple-Data (SIMD) instructions to parallelize the algorithm at the
instruction level.
Package: ssw-align
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
libssw1 (= ${binary:Version})
Description: Smith-Waterman aligner based on libssw
This package provides a command-line aligner based on the libssw library,
a fast SIMD accelerated implementation of the Smith-Waterman algorithm.
The input files can be in FASTA or FASTQ format. Both target and query files
can contain multiple sequences. Each sequence in the query file will be
aligned with all sequences in the target file. Output is provided in SAM or
BLAST-like text format.
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