Currently, .bgz files are read as plain text, which fails due to invalid characters. .bgz files are compatible with gunzip, and have the same data header (0x1F 0x8B). renaming *.bgz files to *.gz files allows them to be decompressed normally.
Adding .bgz to the list of files that can be decompressed by data.table::fread shouldn't require anything other than R.utils. I think adding ".bgz" to the vector in this line:
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if ((w <- endsWithAny(file, c(".gz",".bz2"))) || (gzsig <- identical(head(file_signature, 2L), gz_signature)) || identical(head(file_signature, 3L), bz2_signature)) { |
And checking for w<=2 on this line
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FUN = if (w==1L || gzsig) gzfile else bzfile |
Would allow fread to decompress .bgz files automatically. However, I haven't tested this.
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Currently, .bgz files are read as plain text, which fails due to invalid characters. .bgz files are compatible with gunzip, and have the same data header (0x1F 0x8B). renaming *.bgz files to *.gz files allows them to be decompressed normally.
Adding .bgz to the list of files that can be decompressed by data.table::fread shouldn't require anything other than R.utils. I think adding ".bgz" to the vector in this line:
data.table/R/fread.R
Line 121 in c4a2085
And checking for w<=2 on this line
data.table/R/fread.R
Line 124 in c4a2085
Would allow fread to decompress .bgz files automatically. However, I haven't tested this.