Arbitrary file endings for mapped resources

[mmalenic]

Feature

After mapping a query ID, a file is fetched by appending the file extension based on the query format. For example, a Bam query must have files ending with .bam and their index files must end with .bam.bai. It would be good to allow arbitrary file endings so that files for a given format do not need to be bound to a particular ending.

Motivation

This would be useful for decoupling the location of a file and its index, so that they do not need to be in the same location, or for supporting a storage backend that may not require file endings.

Implementation

A config option could be added that allows setting the file endings for file formats. Or, a query ID could be resolved directly to a file and its index, by having two substitution strings - one for the target file, and one for the index.