December 3, 2015
Viewf053c5f

general cleanup and fixes, doc updates

Michael Lawrence authored on 03/12/2015 21:11:09
May 2, 2014
View96cf993

re-add counting of unique read positions (convenient when dupes are not marked) and fix an uninitialized value (param.cycle_breaks) detected by valgrind

Michael Lawrence authored on 02/05/2014 12:51:58
April 14, 2014
View976c80b

update docs to reflect that the read length is no longer guessed

Michael Lawrence authored on 14/04/2014 20:05:59
April 10, 2014
View6ff8fc3

doc updates

Michael Lawrence authored on 10/04/2014 19:40:59
April 4, 2014
View30f3bfd

drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names)

Michael Lawrence authored on 04/04/2014 13:36:22
Viewae7cf39

bring back the unique read position count, and mean/variance of read positions

Michael Lawrence authored on 04/04/2014 13:16:32
October 14, 2013
View0c27085

doc updates/fixes

Michael Lawrence authored on 14/10/2013 18:52:22
July 14, 2013
View59c3684

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
August 17, 2012
View1650977

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
Viewb22faf0

renaming gmapR2 to gmapR: it lives again

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