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renaming gmapR2 to gmapR: it lives again

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.
Browse code

added TODO

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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+*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.