June 12, 2019
View c3db7e3

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
January 22, 2018
View c087114

follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:24:43
December 3, 2015
View f053c5f

general cleanup and fixes, doc updates

Michael Lawrence authored on 03/12/2015 21:11:09
October 11, 2014
View 2debb80

fix naming of exon_iit argument

Michael Lawrence authored on 11/10/2014 20:33:34
August 11, 2014
View c78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
May 13, 2014
View f5e63d3

update to new bam_tally with support for XS counting, which we now support via BamTallyParam@count_xs.

Michael Lawrence authored on 13/05/2014 02:04:05
April 2, 2014
View 17db5e7

update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)

Michael Lawrence authored on 02/04/2014 22:03:40
October 14, 2013
View 0c27085

doc updates/fixes

Michael Lawrence authored on 14/10/2013 18:52:22
September 20, 2013
View 4d5cc80

update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

Michael Lawrence authored on 20/09/2013 02:05:42
July 14, 2013
View 59c3684

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

Michael Lawrence authored on 14/07/2013 00:43:43
March 26, 2013
View df903e0

Add ignore_duplicate argument to BamTallyParam

Michael Lawrence authored on 26/03/2013 21:40:15
August 17, 2012
View 1650977

Make 'genome' a BamTallyParam slot, instead of a bam_tally argument. This is consistent with GsnapParam. Also, rename 'high_quality_cutoff' to 'high_base_quality'.

Michael Lawrence authored on 17/08/2012 20:19:50
August 2, 2012
View b22faf0

renaming gmapR2 to gmapR: it lives again

Michael Lawrence authored on 02/08/2012 22:24:24