The functions or variables listed here are no longer part
refLocsToLocalLocs has been replaced by
readVcfLongForm has been replaced by
regionFilter have been replaced by
regionFilter has been replaced by
MatrixToSnpMatrix has been replaced by
getTranscriptSeqs has been replaced by
extractTranscriptSeqs in the GenomicFeatures package.
VRangesScanVcfParam has been replaced by
restrictToSVN has been replaced by
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