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Source: htslib
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@debian.org>,
Michael R. Crusoe <crusoe@debian.org>,
Steffen Moeller <moeller@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-exec,
libbz2-dev,
libcurl4-gnutls-dev,
liblzma-dev,
libssl-dev,
zlib1g-dev,
libdeflate-dev
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/htslib
Vcs-Git: https://salsa.debian.org/med-team/htslib.git
Homepage: https://github.com/samtools/htslib
Rules-Requires-Root: no
Package: libhts3
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${misc:Depends},
${shlibs:Depends}
Pre-Depends: ${misc:Pre-Depends}
Replaces: libhts-dev (<< 1.11-3)
Breaks: python-pysam (<< 0.15~),
python3-pysam (<< 0.15~),
libtabixpp (<< 1.0.0-5~),
libhts-dev (<< 1.11-3)
Description: C library for high-throughput sequencing data formats
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
Package: libhts-dev
Architecture: any
Multi-Arch: same
Section: libdevel
Depends: libhts3 (= ${binary:Version}),
libcurl4-gnutls-dev,
libdeflate-dev,
liblzma-dev,
zlib1g-dev,
${misc:Depends}
Description: development files for the HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
.
This package contains development files for the HTSlib: headers, static
library, manual pages, etc.
.
For compatibility with sambamba, the internal routine cram_to_bam was
exported, hereto adopting a patch found in guix.
Package: htslib-test
Architecture: all
Multi-Arch: foreign
Depends: ${misc:Depends},
${perl:Depends}
Breaks: libhts-private-dev
Replaces: libhts-private-dev
Description: Test data for HTSlib
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
Format), used for high-throughput sequencing data, and is the core library
used by samtools and bcftools. HTSlib only depends on zlib. It is known to be
compatible with gcc, g++ and clang.
.
HTSlib implements a generalized BAM (binary SAM) index, with file extension
‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the
new index and then for the old if the new index is absent.
.
This package contains test files and scripts for the HTSlib.
Package: tabix
Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends}
Description: generic indexer for TAB-delimited genome position files
Tabix indexes files where some columns indicate sequence coordinates: name
(usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
like interface. After indexing, tabix is able to quickly retrieve data lines by
chromosomal coordinates. Fast data retrieval also works over network if an URI
is given as a file name.
.
This package is built from the HTSlib source, and provides the bgzip, htsfile,
and tabix tools.
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