April 28, 2010
View892eabd

Fixed bug in readAligned_character() where type="BAM" just returned the function instead of dispatching.

James MacDonald authored on 28/04/2010 17:21:31
April 27, 2010
Viewdf7507d

bug fixes to qa() - calculated perCycle quality Score incorrectly (this was not used in report()) - type=SolexaExportQA mislabelled 'aligned' and 'filtered' reads

Martin Morgan authored on 27/04/2010 19:15:01
April 22, 2010
View79258e8

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/ShortRead@46404 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 22/04/2010 18:36:49
View900598d

Bumped version numbers for BioC 2.6 release

Patrick Aboyoun authored on 22/04/2010 18:21:23
April 13, 2010
View827727e

Add coerce,AlignedRead,GRanges

Michael Lawrence authored on 13/04/2010 19:52:07
April 12, 2010
View63cc00c

avoid unnecessary naming rows of .QA data frames

Martin Morgan authored on 12/04/2010 23:25:32
April 9, 2010
Viewe0273c3

dustyFilter can work in 'batch' mode - some unit test tidy

Martin Morgan authored on 09/04/2010 19:09:29
View95af895

dustyFilter works on DNAStringSet directly, as well as ShortRead*

Martin Morgan authored on 09/04/2010 10:37:17
April 5, 2010
View2ebd044

add readAligned type="BAM"

Martin Morgan authored on 05/04/2010 17:53:56
March 19, 2010
View114a194

Refactored IRanges::resize and reorganized interval methods.

Patrick Aboyoun authored on 19/03/2010 08:01:13
March 12, 2010
View80c2253

Moved the following stuff from BSgenome to the new GenomicRanges package: - seqnames() and seqnames<-() generics; - strand() and strand<-() generics + methods; - GRanges and GRangesList classes + related methods + related unit tests. Updated rtracklayer, GenomicFeatures, ShortRead and Rsamtools accordingly.

Herve Pages authored on 12/03/2010 08:24:05
March 9, 2010
Viewd131490

Removed long deprecated arguments start & end from coverage methods.

Patrick Aboyoun authored on 09/03/2010 18:04:31
February 28, 2010
View879ccad

tidy unit tests

Martin Morgan authored on 28/02/2010 18:43:08
View687a05a

re-level strand() to "+", "-", "*", consistent w/ BSgenome

Martin Morgan authored on 28/02/2010 18:42:45
February 27, 2010
View65dbc11

consistently use Rf_error("'%s' must be '%s'", ...) construct

Martin Morgan authored on 27/02/2010 17:00:29