Bioconductor Code: Browse

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

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

April 14, 2014

	View 6a7e619 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

April 4, 2014

	View 30f3bfd 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
	View ae7cf39 bring back the unique read position count, and mean/variance of read positions Michael Lawrence authored on 04/04/2014 13:16:32

April 2, 2014

	View 17db5e7 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
	View ed089f7 ensure that seqlevel ordering from genome is preserved in result Michael Lawrence authored on 02/04/2014 21:12:52
	View 0fd1d01 be robust to different seqlevel orderings when merging Seqinfo from GmapGenome and BamFile Michael Lawrence authored on 02/04/2014 20:54:46
	View fa1974f tweak consistency checks to allow NA values (when variant_strand=0) Michael Lawrence authored on 02/04/2014 12:58:36

February 28, 2014

	View 7613265 TallyIIT object gains a 'bam' slot, of type BamFile, which is currently used for tracking the seqinfo. Michael Lawrence authored on 28/02/2014 04:44:51

February 18, 2014

	View 1beda81 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