Skip to content

Nicely handle corrupt Minimap2 indexes, build at fetch time? #59

@bede

Description

@bede

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 #58 (comment)

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    enhancementNew feature or request

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions