Bioconductor Code: Browse

April 28, 2010

	View 892eabd Fixed bug in readAligned_character() where type="BAM" just returned the function instead of dispatching. James MacDonald authored on 28/04/2010 17:21:31

April 27, 2010

	View df7507d bug fixes to qa() - calculated perCycle quality Score incorrectly (this was not used in report()) - type=SolexaExportQA mislabelled 'aligned' and 'filtered' reads Martin Morgan authored on 27/04/2010 19:15:01

April 22, 2010

	View 900598d Bumped version numbers for BioC 2.6 release Patrick Aboyoun authored on 22/04/2010 18:21:23

April 12, 2010

	View 63cc00c avoid unnecessary naming rows of .QA data frames Martin Morgan authored on 12/04/2010 23:25:32

April 9, 2010

	View 95af895 dustyFilter works on DNAStringSet directly, as well as ShortRead* Martin Morgan authored on 09/04/2010 10:37:17

April 5, 2010

	View 2ebd044 add readAligned type="BAM" Martin Morgan authored on 05/04/2010 17:53:56

March 19, 2010

	View 114a194 Refactored IRanges::resize and reorganized interval methods. Patrick Aboyoun authored on 19/03/2010 08:01:13

March 12, 2010

	View 80c2253 Moved the following stuff from BSgenome to the new GenomicRanges package: - seqnames() and seqnames<-() generics; - strand() and strand<-() generics + methods; - GRanges and GRangesList classes + related methods + related unit tests. Updated rtracklayer, GenomicFeatures, ShortRead and Rsamtools accordingly. Herve Pages authored on 12/03/2010 08:24:05

March 9, 2010

	View d131490 Removed long deprecated arguments start & end from coverage methods. Patrick Aboyoun authored on 09/03/2010 18:04:31

February 28, 2010

	View 687a05a re-level strand() to "+", "-", "*", consistent w/ BSgenome Martin Morgan authored on 28/02/2010 18:42:45

February 27, 2010

	View c362557 optionally parse SolexaExport multiplex index, paired read, and id - also, use an enum to try to tame field / magic number proliferation Martin Morgan authored on 27/02/2010 16:29:56

February 25, 2010

	View 0b1a568 'renew' as an interface to updating values of ShortRead instances Martin Morgan authored on 25/02/2010 01:24:16

February 8, 2010

	View 06fc53f occurrenceFilter efficiently tests if more reads need including Martin Morgan authored on 08/02/2010 18:16:53

February 7, 2010

	View c45c746 C code tidy, version bump Martin Morgan authored on 07/02/2010 12:38:54
	View df42b6a add occurrenceFilter - flexibly filter reads occurring >=min, <= max number of times - give srrank/srorder/srsort/srduplicated,AlignedRead-method a withSread argument Martin Morgan authored on 07/02/2010 07:18:01