December 3, 2015

general cleanup and fixes, doc updates

Michael Lawrence authored on 03/12/2015 21:11:09
November 13, 2015

fixes for bam_tally update

Michael Lawrence authored on 13/11/2015 22:40:27

work towards supporting new bam_tally; drops quality info (now cutoff based), adds xs/nm/del and codon-level counts

Michael Lawrence authored on 13/11/2015 21:50:11
October 28, 2015

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

Michael Lawrence authored on 28/10/2015 18:51:00
August 7, 2015

labeledLine() was moved from BiocGenerics to S4Vectors

Herve Pages authored on 07/08/2015 23:37:20
April 14, 2015

Reverted to r101133, along with NAMESPACE fixes

Michael Lawrence authored on 14/04/2015 21:40:44

Recent work towards supporting the new features... will revert back to a stable version immediately...

Michael Lawrence authored on 14/04/2015 21:32:10
October 13, 2014

some internal cleanup in BamTallyParam

Michael Lawrence authored on 13/10/2014 18:07:30
August 14, 2014

some fiddling, disable maintainer mode, vbump

Gabriel Becker authored on 14/08/2014 20:39:03
August 11, 2014

add codon tally support. No vbump yet

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

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 30, 2014

add support for the noncovered argument; tells bam_tally to report even those positions that have no coverage

Michael Lawrence authored on 30/04/2014 17:05:27
April 2, 2014

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

labeledLine moved to BiocGenerics

Michael Lawrence authored on 14/10/2013 18:51:25
September 20, 2013

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