May 9, 2019

fix warning on NULL gsnap(input_b=)

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

vectorize over 'output'

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

follow renaming of union classes in S4Vectors

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

add ability to call GMAP

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

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

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

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

fix gsnap for when unique_only is TRUE

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

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

fix gsnap() to take return value from asBam

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

removed option to turn off BAM compression, does not work

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

added support to have bams not sorted

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

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

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

Fix the novesplicing flag to gsnap

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

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

Fix output_path when split_output is FALSE

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