February 1, 2017
Viewe1b17d3

follow renaming of union classes in S4Vectors

Herve Pages authored on 01/02/2017 13:23:02
November 23, 2015
Viewead94b3

add ability to call GMAP

Michael Lawrence authored on 23/11/2015 23:25:34
October 28, 2015
View8418591

resurrect improvements that we reverted before the April release, expect breakage for a while

Michael Lawrence authored on 28/10/2015 18:51:00
April 14, 2015
Viewd5ed124

Reverted to r101133, along with NAMESPACE fixes

Michael Lawrence authored on 14/04/2015 21:40:44
April 12, 2015
Viewe26b36b

no need to declare POSIXlt class

Michael Lawrence authored on 12/04/2015 04:17:43
October 11, 2014
View277f5cf

GsnapOutputList now uses the internal list constructor from S4Vectors (instead of IRanges)

Michael Lawrence authored on 11/10/2014 20:33:08
February 26, 2014
View13cf5e5

fix sam paths for asBam()

Michael Lawrence authored on 26/02/2014 23:11:47
January 14, 2014
View03482b7

GsnapOutput supports the new "circular" outputs

Michael Lawrence authored on 14/01/2014 19:13:26
August 23, 2013
Viewebafcdf

gsnap will now output a GsnapOutputList when there are multiple input files; this means that the return value is more dependent on the input than we may like; perhaps we want a FastqFile and FastqFileList to make this more consistent?

Michael Lawrence authored on 23/08/2013 14:22:00
July 15, 2013
Viewf9d3e36

fix asBam,GsnapOutput for when unique_only is TRUE

Michael Lawrence authored on 15/07/2013 23:42:47
January 29, 2013
Viewf7a6608

Fix asBam,GsnapOutput so that it does not strip the nomapping extension. Also, add validity method that fails when the object points to no sam/bam files.

Michael Lawrence authored on 29/01/2013 00:48:56
January 26, 2013
View2e68fea

Further fixes to asBam,GsnapOutput

Michael Lawrence authored on 26/01/2013 01:59:44
January 25, 2013
View5b410c2

Fix is_dir() call in asBam,GsnapOutput

Michael Lawrence authored on 25/01/2013 03:36:04
November 9, 2012
View59a9b77

GsnapOutput fixes: - Resolve relative paths to absolute in constructor - [single file] Do not include 'sam' extension in bam filename - [single file] asBam updates path to point to bam, instead of sam

Michael Lawrence authored on 09/11/2012 12:54:10
September 19, 2012
View8600ee5

removed option to turn off BAM compression, does not work

Cory Barr authored on 19/09/2012 00:18:48