Bioconductor Code: Browse

April 18, 2014

	View f7ab666 resync with stuff moving from IRanges to S4Vectors Herve Pages authored on 18/04/2014 15:04:25

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 0be2bfb cleanup gmap_build interface, add 'circular' support (automatically derived from BSgenome) and turn off chromosome sorting by default Michael Lawrence authored on 02/04/2014 12:59:22
	View fa1974f tweak consistency checks to allow NA values (when variant_strand=0) Michael Lawrence authored on 02/04/2014 12:58:36

March 10, 2014

	View fab13f0 TP53 genome is now named by the TxDb package from which the TP53 region was retrieved, so that it is automatically refreshed with annotation changes, and devel and release can coexist. Michael Lawrence authored on 10/03/2014 23:10:51

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 26, 2014

	View 13cf5e5 fix sam paths for asBam() Michael Lawrence authored on 26/02/2014 23:11:47

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

February 12, 2014

	View 0379507 clip_overlaps should be clip_overlap Michael Lawrence authored on 12/02/2014 17:13:58

February 7, 2014

	View 7c26346 add calculation of median-distance-from-nearest-end to variantSummary() Michael Lawrence authored on 07/02/2014 01:07:22