./biology/bedtools, Swiss army knife for genome arithmetic

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Branch: CURRENT, Version: 2.31.1, Package name: bedtools-2.31.1, Maintainer: bacon

The bedtools utilities are a suite of tools for performing a wide
range of genomics analysis tasks. The most widely-used of these
tools enable genome arithmetic, i.e., set theory on the genome.
For example, with bedtools one can intersect, merge, count,
complement, and shuffle genomic intervals from multiple files in
common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively
simple task, e.g., intersect two interval files, more sophisticated
analyses can be conducted by stringing together multiple bedtools
operations on the command line or in shell scripts.

Master sites:

Filesize: 20591.768 KB

Version history: (Expand)

CVS history: (Expand)


   2023-11-08 17:46:44 by Jason Bacon | Files touched by this commit (4) | Package updated
Log message:
biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases
   2023-08-14 07:25:36 by Thomas Klausner | Files touched by this commit (1247) 
Log message:
*: recursive bump for Python 3.11 as new default
   2023-06-26 19:21:15 by Jonathan Perkin | Files touched by this commit (1) 
Log message:
bedtools: SunOS needs libsocket.
   2022-06-30 13:19:02 by Nia Alarie | Files touched by this commit (524) 
Log message:
*: Revbump packages that use Python at runtime without a PKGNAME prefix
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2021-02-08 02:49:25 by Jason Bacon | Files touched by this commit (7) 
Log message:
biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
   2021-01-22 18:07:50 by Jason Bacon | Files touched by this commit (6) 
Log message:
biology/bedtools: import bedtools-2.29.2

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.