Sunday, November 4, 2012

Fwd: bedtools - Version 2.17.0, 03-Nov-2012 is OUT! (stats modules start to addup)

Fwd: please follow footer link
bedtools - bedtools: a flexible suite of utilities for comparing genomic features. - Google Project Hosting: Latest news (Version 2.17.0, 03-Nov-2012)
The -split command in intersectBed now applies to both the A and the B file.
New tools: bedtools map, expand, random, makewindows, bamtofastq , jaccard
added -loj (left outer join) option to bedtools intersect. Behaves like a database left join and allows all A intervals to be reported. When overlaps exist, they are reported. When they don't, NULL B entries are reported for the A feature.
Remote BAM files can now be read via HTTP or FTP. Support for remote BED/GFF/VCF will come in a future release.
Added options to "bedtools closest" that ignore up- or down-stream intervals.
Added count_distinct operation to groupby
Added an initial version of a regression testing suite. invoke with "make test"
When using -bed with BAM input in intersectBed, full BED12 features are produced
Developed a standardized API for working with split BED and BAM intervals
Support for "empty" columns: input files with consecutive delimiters are now supported
Github commit number is now included in version number for easier tracking.
Groupby now supports - for stdin
New command line interface invoked with "bedtools command"

(Original Post: https://code.google.com/p/bedtools/.)