Bug 204536

Summary: [NEW] biology/bedtools: Toolset for genome arithmetic
Product: Ports & Packages Reporter: scottcheloha
Component: Individual Port(s)Assignee: Wen Heping <wen>
Status: Closed FIXED    
Severity: Affects Only Me CC: wen
Priority: --- Keywords: feature, needs-qa, patch
Version: Latest   
Hardware: Any   
OS: Any   
Description Flags
shar(1) of biology/bedtools; Makefile, distinfo, pkg-plist, pkg-descr, and a small patch in files/ none

Description scottcheloha 2015-11-14 05:22:54 UTC
Created attachment 163109 [details]
shar(1) of biology/bedtools; Makefile, distinfo, pkg-plist, pkg-descr, and a small patch in files/

Bedtools performs common set arithmetic tasks on genomes.  Each subtool performs a relatively simple task---intersection, complementation, etc.---on the input genome(s), and arbitrarily complex manipulations and analyses are possible through the creation of shell scripts that string these operations together.
Comment 1 commit-hook freebsd_committer 2016-01-19 08:57:01 UTC
A commit references this bug:

Author: wen
Date: Tue Jan 19 08:56:35 UTC 2016
New revision: 406676
URL: https://svnweb.freebsd.org/changeset/ports/406676

  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.

  WWW: http://bedtools.readthedocs.org/

  PR:		204536
  Submitted by:	scottcheloha@gmail.com