bede
Nicely handle corrupt Minimap2 indexes, build at fetch time?
Since 2.0.0, MMI files are created on the fly if they do not already exist when hostile clean is invoked. In subsequent runs the .mmi version of the index is detected and used automatically, saving time. If MMI construction is interrupted the file can be corrupted, leading to repeated failure of hostile clean. This likely happened in https://github.com/bede/hostile/issues/58#issuecomment-2748869980
There needs to be an easy way to purge corrupt MMI indexes, ideally without forcing redownload of fasta(.gz) indexes.
MMI creation should probably happen at fetch time instead, which seems more atomic.
We already have hostile index delete --mmi for this, but could still push mmi construction to fetch time
MMIs could also be built with a different file extension and renamed, as a transaction of sorts indicating completion