data.table::fread can't handle .bgz files by default. This means all functions that rely on it (read_sumstats, read_header) fail for many tabix-indexed files.
Made changes throughout the code to detect and import bgz files with the following trick:
path <- "filepath.tsv.bgz"
dat <- data.table::fread(cmd=paste("gunzip -c",path))
My only concern is that gunzip might not be installed on every machine, though I think gzip (which its part of) comes standard with most OS.
data.table::freadcan't handle .bgz files by default. This means all functions that rely on it (read_sumstats,read_header) fail for many tabix-indexed files.Made changes throughout the code to detect and import bgz files with the following trick:
My only concern is that
gunzipmight not be installed on every machine, though I thinkgzip(which its part of) comes standard with most OS.