November 13, 2015
View685d60e

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
Viewf51bc89

Update gstruct (bam_tally)

Michael Lawrence authored on 28/10/2015 20:55:30
View8418591

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
Viewd5ed124

Reverted to r101133, along with NAMESPACE fixes

Michael Lawrence authored on 14/04/2015 21:40:44
Viewc8fd96e

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
March 25, 2015
Viewf58d4e9

update gstruct/bamtally

Michael Lawrence authored on 25/03/2015 20:25:05
August 26, 2014
View52563ef

incorporate Tom's bugfix to bamtally when there are no reads at a position. Fixes segfault in R CMD check VariantTools

Gabriel Becker authored on 26/08/2014 20:33:39
August 11, 2014
Viewc78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
June 6, 2014
View52b3ca6

update gstruct (hopefully fix build)

Michael Lawrence authored on 06/06/2014 22:10:15
June 4, 2014
View2a4fd1e

update ignores

Michael Lawrence authored on 04/06/2014 23:34:39
May 13, 2014
Viewf5e63d3

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
May 5, 2014
View9f0e3a7

bam_tally has reworked memory management to avoid memory "leaks" that seem to happen on our cluster

Michael Lawrence authored on 05/05/2014 21:02:45
April 30, 2014
View144f6bb

update bam_tally, mostly to fix memory leaks but we are also moving towards a decent indel realigner

Michael Lawrence authored on 30/04/2014 17:04:17
April 2, 2014
View17db5e7

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
January 15, 2014
Viewd78ea58

update bam_tally source for fix to quality tabulation

Michael Lawrence authored on 15/01/2014 21:39:44