options(stringsAsFactors = F)
i <- "hg19_intervar_20170202.txt"
cat(sprintf('File:%s', i), sep = "\n")
db <- str_replace(i, fixed(".txt"), "")
cat(sprintf('DB:%s', db), sep = "\n")
cat(sprintf('Dat:%s', i), sep = "\n")
db.sqlite <- paste0(db, ".sqlite")
unlink(db.sqlite), db.sqlite, db, verbose = T)
cols <- c('#Chr', 'Start')
sqlite.index(db.sqlite, db, "chr_start_index", cols, verbose = T)

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annovarR documentation built on Jan. 9, 2018, 5:05 p.m.