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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Error on invalid interleaved input #1436

Open glennhickey opened 6 years ago

glennhickey commented 6 years ago

When running vg map/mpmap (soon surject too #1432) in interleaved mode on GAMs, there's no error if the GAM is not interleaved. It just takes one missing made to throw off the entire file. This can happen when, say, the GAM was extracted from Rocksdb for a region (ex with vg chunk).

From experience, this type of error is pretty costly in terms of time to track down. So I think it'd be pretty valuable to have a little check when scanning interleaved GAMs to make sure the fragment names match up.

jeizenga commented 6 years ago

Checking the names seems like of fragile to me. Like, are we going to enforce one naming convention?

glennhickey commented 6 years ago

Don't need a convention, just a check to make sure fragment_next/prev match up.

On Sat, Feb 10, 2018 at 3:04 PM, Jordan Eizenga notifications@github.com wrote:

Checking the names seems like of fragile to me. Like, are we going to enforce one naming convention?

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