Package: genomicsdb-tools (1.5.4-1 and others)

Links for genomicsdb-tools

Debian Resources:

Download Source Package genomicsdb:

Maintainers:

External Resources:

Homepage [www.genomicsdb.org]

Similar packages:

sparse array storage library for genomics (tools)

GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data.

The GenomicsDB stores variant data in a 2D array where:

 - Each column corresponds to a genomic position (chromosome + position);
 - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH
   terminology);
 - Each cell contains data for a given sample/CallSet at a given position;
   data is stored in the form of cell attributes;
 - Cells are stored in column major order - this makes accessing cells with
   the same column index (i.e. data for a given genomic position over all
   samples) fast.
 - Variant interval/gVCF interval data is stored in a cell at the start of the
   interval. The END is stored as a cell attribute. For variant intervals
   (such as deletions and gVCF REF blocks), an additional cell is stored at
   the END value of the variant interval. When queried for a given genomic
   position, the query library performs an efficient sweep to determine all
   intervals that intersect with the queried position.

This package contains some tools to be run as executable files.

Other Packages Related to genomicsdb-tools

depends

recommends

suggests

enhances

dep: libc6 (>= 2.38) [not alpha, sh4]

GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb

dep: libc6 (>= 2.39) [sh4]
dep: libc6.1 (>= 2.38) [alpha]

GNU C Library: Shared libraries
also a virtual package provided by libc6.1-udeb
dep: libfmt9 (>= 9.1.0+ds1)

fast type-safe C++ formatting library -- library
dep: libgcc-s1 (>= 3.0) [amd64]

GCC support library

dep: libgcc-s1 (>= 3.4) [alpha]

dep: libgcc-s1 (>= 4.2) [sh4]

dep: libgcc-s1 (>= 4.5) [mips64el]
dep: libgcc-s2 (>= 4.2.1) [m68k]

GCC support library
dep: libgenomicsdb1 (= 1.5.3-3+b1) [alpha, sh4]

sparse array storage library for genomics (shared libraries)

dep: libgenomicsdb1 (= 1.5.4-1) [not alpha, sh4]
dep: libgomp1 (>= 4.9)

GCC OpenMP (GOMP) support library
dep: libmpich12 [m68k, sh4]

Shared libraries for MPICH
dep: libopenmpi3t64 (>= 5.0.5) [not m68k, sh4]

high performance message passing library -- shared library
dep: libprotobuf23 (>= 3.12.4) [alpha]

protocol buffers C++ library
dep: libprotobuf32t64 (>= 3.21.12) [not alpha]

protocol buffers C++ library
dep: libstdc++6 (>= 13.1) [m68k]

GNU Standard C++ Library v3

dep: libstdc++6 (>= 14) [not m68k]
dep: libuuid1 (>= 2.16)

Universally Unique ID library

Download genomicsdb-tools

Download for all available architectures
Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.5.3-3+b1	1,597.4 kB	15,049.0 kB	[list of files]
amd64	1.5.4-1	1,653.7 kB	13,175.0 kB	[list of files]
m68k (unofficial port)	1.5.4-1	1,543.4 kB	12,323.0 kB	[list of files]
mips64el	1.5.4-1	1,492.0 kB	18,407.0 kB	[list of files]
sh4 (unofficial port)	1.5.3-3+b1	1,685.8 kB	11,882.0 kB	[list of files]