April 5, 2016
View 8b7fd7a

adjustments in response to the vals -> filter renaming in GenomicFeatures

Herve Pages authored on 05/04/2016 22:55:27
October 28, 2015
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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
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Reverted to r101133, along with NAMESPACE fixes

Michael Lawrence authored on 14/04/2015 21:40:44
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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 11, 2014
View c78be69

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
May 13, 2014
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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
April 2, 2014
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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
March 10, 2014
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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 12, 2014
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clip_overlaps should be clip_overlap

Michael Lawrence authored on 12/02/2014 17:13:58
January 14, 2014
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vignette improvements

Michael Lawrence authored on 14/01/2014 19:15:01
September 25, 2013
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call Rcode{} instead of code{}

Dan Tenenbaum authored on 25/09/2013 20:07:03
September 20, 2013
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update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

Michael Lawrence authored on 20/09/2013 02:05:42
July 14, 2013
View 59c3684

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

Michael Lawrence authored on 14/07/2013 00:43:43
November 28, 2012
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dropped size of kmer from 15 down to 12 for creation of GmapGenome object in vignette for the purpose of reducing memory footprint so gmapR builds on modern Macbooks

Cory Barr authored on 28/11/2012 22:29:13
November 27, 2012
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*Hutch's Mac build machine was running out of memory during build. Reduced the memory footprint used by lowering the k-mer size used for creating the fly GmapGenome in the vignette.

Cory Barr authored on 27/11/2012 19:34:50