git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 02/08/2012 22:24:24
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-*use BSGenome and Bioc dbSNP objects instead of downloading from UCSC. |
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+*GmapGenome doesn't yet have a method for DNAStringSet genomes |
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-*globals function needs to set elements in the list returned by |
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- options() instead of using the globals() fun. Other wise |
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- HTSeqGenieBase and gmapR will both have exported globals() functions |
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+*genome param for GmapGenome class isn't making it into the |
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+object. not in representation? |
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-*HTSeqGenieBase needs to depend on gmapR and not contain now-redundant |
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- code. To to this, HTSeqGenieBase::globals() needs to have entries |
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- removed now in gmapR::globals() |
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+*passing use_snps=NULL as an arg to GsnapParam constructor breaks it |
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-*configureGmapR.R calls buildGmapIndex, buildGmapDbSNPIndex, and |
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-buildRefseqSpliceSites. These are high-level functions that obtain |
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-hg19 data and call more generalized functions. These high-level |
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-functions belong in HTSeqGenieBase. |
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+*fix extra() arg in gsnap method |
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+ |
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+*Vignette |
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+**remove all eval=FALSE. This means rolling some GmapGenome packages |
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+ |
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+*cannot overwrite files from gsnap. In other words, can only run gsnap |
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+ function once. |
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+ |
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+*make sure mapping in gsnap command-line too (short form args) are |
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+ clearly linked to in the R docs (Greg request) |
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+ |
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+*get NGS seq pipeline tests working |
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+ |
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+*gsnap said the distant_splice_identity args is not supported, but |
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+ it's in the gsnap --help documention |
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+ |
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+*bam_tally segfaults if the BAM file used is not indexed |
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+ |
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+*cannot get seqinfo(GmapGenome) if genome created with |
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+ DNAStringSet. Also, R issues warnings during creation about |
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+ contigs. Currently, the unity test for seqinfo(GmapGenome) does not |
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+ exist because of this. |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@58341 bc3139a8-67e5-0310-9ffc-ced21a209358
Cory Barr authored on 23/09/2011 18:02:46
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new file mode 100755 |
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@@ -0,0 +1,14 @@ |
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+*use BSGenome and Bioc dbSNP objects instead of downloading from UCSC. |
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+ |
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+*globals function needs to set elements in the list returned by |
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+ options() instead of using the globals() fun. Other wise |
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+ HTSeqGenieBase and gmapR will both have exported globals() functions |
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+ |
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+*HTSeqGenieBase needs to depend on gmapR and not contain now-redundant |
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+ code. To to this, HTSeqGenieBase::globals() needs to have entries |
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+ removed now in gmapR::globals() |
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+ |
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+*configureGmapR.R calls buildGmapIndex, buildGmapDbSNPIndex, and |
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+buildRefseqSpliceSites. These are high-level functions that obtain |
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+hg19 data and call more generalized functions. These high-level |
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+functions belong in HTSeqGenieBase. |