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gt1 / biobambam2

Tools for early stage alignment file processing
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Is REF_PATH/REF_CACHE used for reading CRAM? #68

Open keiranmraine opened 6 years ago

keiranmraine commented 6 years ago

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 commented 6 years ago

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.