I have a bit of an unusual situation. Because of things that are out of my control, all of my input bgen and index files are in individual directories.
I’m wondering if it’s possible for the bgen and index files to be in different directories. I thought that the
index_file_map could be the option but I’m having trouble getting things to work.
bgen_index_map = dict([("data/bgen/chr22.bgen", "data/index/chr22.bgen.idx")]) mt = hl.import_bgen(path = "data/bgen/chr22.bgen", entry_fields = ["GP"], index_file_map = bgen_index_map) > 2018-11-30 20:22:22 Hail: WARN: BGEN file `data/bgen/chr22.bgen' contains no sample ID block and no sample ID file given. > Using _0, _1, ..., _N as sample IDs. > 2018-11-30 20:22:22 Hail: INFO: Number of BGEN files parsed: 1 > 2018-11-30 20:22:22 Hail: INFO: Number of samples in BGEN files: 487409 > 2018-11-30 20:22:22 Hail: INFO: Number of variants across all BGEN files: 1255683
These commands run without error but if I try and do anything, I get a fatal error.
mt.s.show(5) > FatalError: FileNotFoundException: data/bgen/chr22.bgen.idx
The error message makes it seems like hail still looks for the index file in the same directory as the bgen file.
Any help with this would be great.