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.
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 Log: 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 Changes: head/biology/Makefile head/biology/bedtools/ head/biology/bedtools/Makefile head/biology/bedtools/distinfo head/biology/bedtools/files/ head/biology/bedtools/files/patch-Makefile head/biology/bedtools/pkg-descr head/biology/bedtools/pkg-plist