April 4, 2014
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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
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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
January 14, 2014
View 4f9f81f

update docs for change to output path determination

Michael Lawrence authored on 14/01/2014 19:12:33
October 14, 2013
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doc updates/fixes

Michael Lawrence authored on 14/10/2013 18:52:22
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
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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
March 27, 2013
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Add GmapGenome->DNAStringSet coercion, exports the whole genome sequence. This means export(x, "genome.fasta") should work.

Michael Lawrence authored on 27/03/2013 19:11:09
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Make seqinfo(x) the default for 'which' in getSeq,GmapGenome

Michael Lawrence authored on 27/03/2013 18:47:53
March 26, 2013
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Add getSeq,GmapGenome method

Michael Lawrence authored on 26/03/2013 21:44:17
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Add ignore_duplicate argument to BamTallyParam

Michael Lawrence authored on 26/03/2013 21:40:15
September 18, 2012
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GsnapParam docs for 'mode' arg described valuse from old version of gsnap

Cory Barr authored on 18/09/2012 21:41:05
September 12, 2012
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added aliases to remove last of WARNINGs

Cory Barr authored on 12/09/2012 23:25:14
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*drop passing of ... arg to method snps<- eventually dispatches on

Cory Barr authored on 12/09/2012 22:29:42
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doc aliases added to reduced WARNINGs in R CMD check

Cory Barr authored on 12/09/2012 20:23:54