Feature Request: check for gencode while creating index

[alexvpickering]

This came up in #336

When building a gencode-based index with salmon index without the --gencode flag, the index that is generated won't work when subsequently running e.g. salmon alevin. This can be a pain to figure out the mistake (missing --gencode flag).

Perhaps some sort of quick grep of the index file name for 'gencode' or within the file for multiple '|'s (used for gencode field separator but not ensembl) should be done to check if it's gencode followed by a warning/error if the --gencode flag is missing? Another possibility could be to just auto-detect if the index is gencode using the above tests, removing the need for the --gencode flag. Thank you

[k3yavi]

Thanks again @alexvpickering .
We have fixed this in the develop branch and it will be part of the salmon from the next release which we plan to release very soon.

[rob-p]

Now (since v0.14.0), the index command will issue a warning if you don't pass --gencode but the fasta being indexed looks to be gencode.