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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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Harmonize getSeqNames(), getSequenceNames() and getTargetNames() #3

Closed HenrikBengtsson closed 9 years ago

HenrikBengtsson commented 9 years ago

We currently have:

> methods("getSeqNames")
[1] getSeqNames.Bowtie2IndexSet    getSeqNames.FastaReferenceFile
[3] getSeqNames.GtfDataFile
> methods("getSequenceNames")
[1] getSequenceNames.Bowtie2IndexSet
> methods("getTargetNames")
[1] getTargetNames.BamDataFile

TO DO: Make all use getSeqNames().

HenrikBengtsson commented 9 years ago

getSequenceNames() for Bowtie2IndexSet was already deprecated. Removing it.

HenrikBengtsson commented 9 years ago

getSeqNames() for BamDataFile now calls getTargetNames(); keeping the latter because there are several getTarget*() function which seems to be named after BAM conventions.