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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

bamtools 2.5.1+dfsg-3

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One-liner (summary)

toolkit for manipulating BAM (genome alignment) files

Description

BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the bamtools command-line toolkit.

Available bamtools commands: convert Converts between BAM and a number of other formats count Prints number of alignments in BAM file(s) coverage Prints coverage statistics from the input BAM file filter Filters BAM file(s) by user-specified criteria header Prints BAM header information index Generates index for BAM file merge Merge multiple BAM files into single file random Select random alignments from existing BAM file(s), intended more as a testing tool. resolve Resolves paired-end reads (marking the IsProperPair flag as needed) revert Removes duplicate marks and restores original base qualities sort Sorts the BAM file according to some criteria split Splits a BAM file on user-specified property, creating a new BAM output file for each value found stats Prints some basic statistics from input BAM file(s)

License

Unknown

Size

147.0 KB

Downloads

Status	Completed
Checksum (MD5)	8558d4d62590035575b09e489f67c323
Checksum (SHA-1)	97454476344cdfca4b0c4bc1a693a4105158612f
Checksum (SHA-256)	55896a2e99e659ca69624967065528c2ffe642a6eac14296431ae91d343a1656
Checksum (SHA-512)	f689b9adbb7d0bd0f629450f656692072e7295be354b5b4a65b0074ebd9c5d029d…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	9 months, 2 weeks ago
Uploaded By
Slug Id	bamtools_251dfsg-3_armhfdeb-p0pr
Unique Id	ExQ9PgYPnIBi
Version (Raw)	2.5.1+dfsg-3
Version (Parsed)	Major: 2 Minor: 5 Patch: 1 Type: SemVer (Strict) Metadata: dfsg-3
	extended metadata
Homepage	https://github.com/pezmaster31/bamtools/wiki
Installed Size	371.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

73fdc89006c6041361a40408a67f88a7

Depends	libbamtools2.5.1
Depends	libc6	>=2.4
Depends	libgcc1	>=1:3.5
Depends	libjsoncpp1	>=1.7.4
Depends	libstdc++6	>=5.2

You can embed a badge in another website that shows this or the latest version of this package.

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[![This version of 'bamtools' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'bamtools' @ Cloudsmith|
.. |This version of 'bamtools' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'bamtools' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/2.5.1+dfsg-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'bamtools' @ Cloudsmith" /></a>

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[![Latest version of 'bamtools' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'bamtools' @ Cloudsmith|
.. |Latest version of 'bamtools' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'bamtools' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/bamtools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'bamtools' @ Cloudsmith" /></a>

rendered as:

These instructions assume you have setup the repository first (or read it).

To install/use bamtools @ version 2.5.1+dfsg-3 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install bamtools=2.5.1+dfsg-3

Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

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