Is REF_PATH/REF_CACHE used for reading CRAM?

[keiranmraine]

In the readme you indicate the REF_PATH/REF_CACHE variables are used for cram output.

https://github.com/gt1/biobambam2#bamsormadup-and-cram-output

Can you clarify if they are used when reading CRAM as well? When receiving data from others in CRAM it would be helpful if we didn't need to request the reference when it can be auto discovered from ENA.

[EvanTheB]

Just my observation:
io_lib (aka scramble) is used for reading CRAM, it checks for REF_CACHE and REF_PATH: https://github.com/jkbonfield/io_lib/blob/d4db6015ba8b6ec78e95895242b2d34b15dfa83b/io_lib/cram_io.c#L2781

There is some code in biobambam + libmaus reference these environment variables, but I think they are just for error messages.