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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. |
