November 13, 2015

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
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
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
February 7, 2014

add calculation of median-distance-from-nearest-end to variantSummary()

Michael Lawrence authored on 07/02/2014 01:07:22
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
March 26, 2013

Add R_Genome_getSeq for efficiently retrieving sequence from a GMAP genome index. This is super fast.

Michael Lawrence authored on 26/03/2013 21:38:39
September 25, 2012

Decoupling the bam tallying from summarization. Soon, we will return an IIT, which can be summarized in various ways. Currently, the only way is the variant summary.

Michael Lawrence authored on 25/09/2012 16:00:17
August 2, 2012

renaming gmapR2 to gmapR: it lives again

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