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
November 2, 2015
Viewf18ff85

more robust check for empty read pos breaks

Michael Lawrence authored on 02/11/2015 22:42:05
Viewbfeb9ea

fix forwarding args to TallyIIT

Michael Lawrence authored on 02/11/2015 21:40:00
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
August 13, 2014
View085e7d8

fix change of cds_iit to exon_iit

Gabriel Becker authored on 13/08/2014 20:26:10
August 11, 2014
Viewc78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
July 25, 2014
View6f40570

fix typo in VCF FORMAT header for read.pos.mean.ref

Michael Lawrence authored on 25/07/2014 20:15:30
May 16, 2014
Viewab8835c

fix seqinfo merging in variantSummary

Michael Lawrence authored on 16/05/2014 21:33:43
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
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 30, 2014
View6d5d75f

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 14, 2014
View6a7e619

disable read length guessing; just expect the user to provide it when they need the statistics that depend on it

Michael Lawrence authored on 14/04/2014 19:50:15