[Bioc-devel] VcfFile and VcfFileList

Robert Castelo robert.castelo at upf.edu
Wed Jul 17 12:22:06 CEST 2013


i'm interested in having classes 'VcfFile' and 'VcfFileList', analogous 
to 'BamFile'/'BamFileList' or 'Bcf/BcfFileList,' with their 
corresponding functionality to ease manipulating, in this case, VCF 
files. i thought i could sort of copy&paste code from Rsamtools but the 
existing definitions of classes and methods rely on the Rsamtools 
internal functions '.RsamtoolsFile' and '.RsamtoolsFileList' which are 
not exported, and thus i cannot use them.

i might be following the wrong path, so i'd like to ask how should i 
proceed to have this kind of functionality to handle VCF files, 
analogous to the existing one in Rsamtools to handle BAM or BCF files.


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