Ubuntu
genomicsdb package

genomicsdb 1.5.0-2 source package in Ubuntu

Changelog

genomicsdb (1.5.0-2) unstable; urgency=medium

  * Allowing the package to build against catch2 3.x (Closes: #1054675)

 -- Pierre Gruet <email address hidden>  Fri, 03 Nov 2023 17:16:04 +0100

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Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
any all
Section:
misc
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Noble release universe misc

Downloads

File Size SHA-256 Checksum
genomicsdb_1.5.0-2.dsc 3.3 KiB e97403ad4889ab899e5c22cc60f17ca08bba1fff7344dd08115f45b814f580c9
genomicsdb_1.5.0.orig-genomicsdb-htslib.tar.gz 1.4 MiB 32483d1b3a37559e0f328af27a8ec67197606899796dd4e580612bd6f32cd9f3
genomicsdb_1.5.0.orig-genomicsdb-tiledb.tar.gz 917.3 KiB 7f0a515c2df104432079b8ea46794ee693822d547f68f36532db39203ac1d78f
genomicsdb_1.5.0.orig.tar.gz 6.4 MiB 41a6dec4a8e198b464716142c8b5ae06650311edfa50987907eac15240574e78
genomicsdb_1.5.0-2.debian.tar.xz 25.6 KiB fd79636be7889c38f9d5770282c9c115e90db3271568c562497341c3ecac56b3

Available diffs

No changes file available.

Binary packages built by this source

genomicsdb-tools: 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.

genomicsdb-tools-dbgsym: debug symbols for genomicsdb-tools
libgenomicsdb-dev: sparse array storage library for genomics (development files)

 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 the development files and the static library.

libgenomicsdb-jni: sparse array storage library for genomics (Java native bindings)

 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 the Java native bindings.

libgenomicsdb-jni-dbgsym: debug symbols for libgenomicsdb-jni
libgenomicsdb0: sparse array storage library for genomics (shared libraries)

 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 the shared library.

libgenomicsdb0-dbgsym: debug symbols for libgenomicsdb0