May 9, 2019
View 6d010e6

fix warning on NULL gsnap(input_b=)

Michael Lawrence authored on 09/05/2019 17:18:57
May 17, 2017
View 3854987

vectorize over 'output'

Michael Lawrence authored on 17/05/2017 20:11:24
February 1, 2017
View e1b17d3

follow renaming of union classes in S4Vectors

Herve Pages authored on 01/02/2017 13:23:02
November 23, 2015
View ead94b3

add ability to call GMAP

Michael Lawrence authored on 23/11/2015 23:25:34
January 14, 2014
View 563f6d6

gsnap() derives default output path from the current working directory

Michael Lawrence authored on 14/01/2014 19:12:06
August 23, 2013
View ebafcdf

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
View 298febc

fix gsnap for when unique_only is TRUE

Michael Lawrence authored on 15/07/2013 23:39:06
February 28, 2013
View 273e823

Add low-level ..gsnap() interface to gsnap that accepts an argument string (instead of building that string from its formal arguments, like .gsnap). Also checks for whether gsnap succeeds.

Michael Lawrence authored on 28/02/2013 23:03:33
November 9, 2012
View 97bd8ae

fix gsnap() to take return value from asBam

Michael Lawrence authored on 09/11/2012 12:55:36
September 19, 2012
View 8600ee5

removed option to turn off BAM compression, does not work

Cory Barr authored on 19/09/2012 00:18:48
September 14, 2012
View 9f41c85

added support to have bams not sorted

Cory Barr authored on 14/09/2012 23:17:11
September 11, 2012
View 297de88

*gmapR option name for returning system calls is now "systemCallMode"

Cory Barr authored on 11/09/2012 22:12:30
View 7f5a962

Fix the novesplicing flag to gsnap

Michael Lawrence authored on 11/09/2012 18:50:23
View 1116df9

added capability to overwrite .system via providing a function to options('gmapRSysCall')

Cory Barr authored on 11/09/2012 02:32:47
September 7, 2012
View 835aba9

Fix output_path when split_output is FALSE

Michael Lawrence authored on 07/09/2012 22:03:43