October 13, 2014
View 60982df

some internal cleanup in BamTallyParam

Michael Lawrence authored on 13/10/2014 18:07:30
October 11, 2014
View 277f5cf

GsnapOutputList now uses the internal list constructor from S4Vectors (instead of IRanges)

Michael Lawrence authored on 11/10/2014 20:33:08
View 555225f

allow genomes to be built from any sequence file supported by rtracklayer

Michael Lawrence authored on 11/10/2014 18:17:31
September 5, 2014
View 9aca6bd

generalize TP53Genome to GeneGenome, which takes a character vector of gene names

Michael Lawrence authored on 05/09/2014 21:50:22
August 14, 2014
View cfb01d1

some fiddling, disable maintainer mode, vbump

Gabriel Becker authored on 14/08/2014 20:39:03
August 13, 2014
View 085e7d8

fix change of cds_iit to exon_iit

Gabriel Becker authored on 13/08/2014 20:26:10
August 11, 2014
View c78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
July 28, 2014
View c0cce6c

follow renaming of TranscriptDb class -> TxDb

Herve Pages authored on 28/07/2014 23:15:59
July 25, 2014
View 6f40570

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

Michael Lawrence authored on 25/07/2014 20:15:30
May 16, 2014
View ab8835c

fix seqinfo merging in variantSummary

Michael Lawrence authored on 16/05/2014 21:33:43
May 13, 2014
View f5e63d3

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
View 3b5cad5

add internal function for getting transcripts on the TP53 genome

Michael Lawrence authored on 13/05/2014 02:02:31
May 5, 2014
View 9f0e3a7

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
View 96cf993

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
View 6d5d75f

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