May 20, 2020
Viewfc4e9f8

Repair subsetByOverlaps() on hasGRanges derivatives

Hervé Pagès authored on 20/05/2020 22:23:58
October 16, 2017
View94da5a9

resolving conflicts:

Kasper Daniel Hansen authored on 16/10/2017 18:53:15
September 18, 2017
View8f4b326

- Use new 'maxgap' and 'minoverlap' defaults in "findOverlaps" method for hasGRanges objects. - Remove "subsetByOverlaps" methods for hasGRanges objects. They are redundant with the default "subsetByOverlaps" method defined in the IRanges package. The default method works out-of-the-box on any object that supports findOverlaps() and linear subsetting ([), which is the case for hasGRanges objects.

Hervé Pagès authored on 18/09/2017 15:02:27
March 10, 2016
View5e9d3da

merge conflicts

Kasper D. Hansen authored on 10/03/2016 02:44:17
View8657761

merge conflicts

khansen authored on 10/03/2016 02:44:17
December 16, 2015
Viewa4efefe

findOverlaps() and subsetByOverlaps() have no 'algorithm' argument anymore

Herve Pages authored on 16/12/2015 21:21:51
Viewcc7c8a0

findOverlaps() and subsetByOverlaps() have no 'algorithm' argument anymore

hpages@fhcrc.org authored on 16/12/2015 21:21:51
December 5, 2014
Viewc651329

add 'algorithm' arg to "subsetByOverlaps" methods

Herve Pages authored on 05/12/2014 06:42:18
View0a6cbe0

add 'algorithm' arg to "subsetByOverlaps" methods

hpages@fhcrc.org authored on 05/12/2014 06:42:18
View8f99870

change 'algorithm' default from "intervaltree" to "nclist"

Herve Pages authored on 05/12/2014 06:14:38
View3fedb39

change 'algorithm' default from "intervaltree" to "nclist"

hpages@fhcrc.org authored on 05/12/2014 06:14:38
November 8, 2014
View40dc11d

The findOverlaps() generic got a new 'algorithm' argument in IRanges 2.1.10 (commit 96627). So add it to all "findOverlaps" methods defined in bsseq.

Herve Pages authored on 08/11/2014 02:53:46
View1d865e3

The findOverlaps() generic got a new 'algorithm' argument in IRanges 2.1.10 (commit 96627). So add it to all "findOverlaps" methods defined in bsseq.

hpages@fhcrc.org authored on 08/11/2014 02:53:46
October 4, 2013
View8e5853a

Version bump; various fixes to address issues reported by R CMD check, including documentation, use of :::, and deprecation of seqselect

Kasper D. Hansen authored on 04/10/2013 15:23:24
View1824727

Version bump; various fixes to address issues reported by R CMD check, including documentation, use of :::, and deprecation of seqselect

khansen authored on 04/10/2013 15:23:24