February 1, 2016
View12074fe

stream past XS counts for indels (even when XS counting is disabled)

Michael Lawrence authored on 01/02/2016 20:11:05
November 24, 2015
View5659f09

add raw total count statistic to tallies (everything else now qual filtered)

Michael Lawrence authored on 24/11/2015 22:19:59
November 13, 2015
View38518dd

fixes for bam_tally update

Michael Lawrence authored on 13/11/2015 22:40:27
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
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
Viewe01ded3

just some reformatting / cleanup

Michael Lawrence authored on 25/03/2015 02:12:41
August 11, 2014
Viewc78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
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 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 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
February 18, 2014
View18fc48e

remove some unnnecessary code from tally summarization

Michael Lawrence authored on 18/02/2014 21:37:13
View1beda81

drop unique read position count and mean/variance of read positions from statistics output by bam_tally

Michael Lawrence authored on 18/02/2014 21:24:22