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View ae7cf39
bring back the unique read position count, and mean/variance of read positionsMichael Lawrence authored on 04/04/2014 13:16:32 |
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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 |
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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 |
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View 4f9f81f
update docs for change to output path determinationMichael Lawrence authored on 14/01/2014 19:12:33 |
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View 0c27085
doc updates/fixesMichael Lawrence authored on 14/10/2013 18:52:22 |
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View 4d5cc80
update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tallyMichael Lawrence authored on 20/09/2013 02:05:42 |
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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 |
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View 2f697ca
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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View 8edb187
Make seqinfo(x) the default for 'which' in getSeq,GmapGenomeMichael Lawrence authored on 27/03/2013 18:47:53 |
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View 5db28c4
Add getSeq,GmapGenome methodMichael Lawrence authored on 26/03/2013 21:44:17 |
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View df903e0
Add ignore_duplicate argument to BamTallyParamMichael Lawrence authored on 26/03/2013 21:40:15 |
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View aec742f
GsnapParam docs for 'mode' arg described valuse from old version of gsnapCory Barr authored on 18/09/2012 21:41:05 |
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View 5ed9345
added aliases to remove last of WARNINGsCory Barr authored on 12/09/2012 23:25:14 |
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View 15766c6
*drop passing of ... arg to method snps<- eventually dispatches onCory Barr authored on 12/09/2012 22:29:42 |
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View 10a5cab
doc aliases added to reduced WARNINGs in R CMD checkCory Barr authored on 12/09/2012 20:23:54 |