Question Ragtag scaffold command parameters

[Saveli01]

When I use this command:

ragtag.py scaffold -u -w -r -g 1 drosophila_reference.fasta DROS_scaf.fasta

The gap lengths work perfectly for length = 2 or higher. But when the gap has an expected length=1, the returned gap length = 100. (this is the default).

Any idea why this happens or what parameters would correctly return a gap of just one base?

[malonge]

Hi there,

Yes it looks like 2 is the minimum:

https://github.com/malonge/RagTag/blob/11f670b373fbbd4139df470ac676943665ac0f18/ragtag_scaffold.py#L528

I don't know why I did it this way ... I will leave this as a feature request for the next RagTag update. Unless I can remind myself why I set 2 as the minimum, I can easily change this to allow for gaps of size 1.

[Saveli01]

Great, thanks for confirming, and also for pointing to the relevant section of the code. Could you tell me which line(s) you would change? I can make that change myself and use it locally until the next update is ready.

[malonge]

I think it should work if you change:

if i_gap_size <= min_gap_size:

to

if i_gap_size < min_gap_size:

on line 529

[Saveli01]

Thank you!

On Sun, Feb 6, 2022 at 5:30 PM Michael Alonge @.***> wrote:

I think it should work if you change:

if i_gap_size <= min_gap_size:

to

if i_gap_size < min_gap_size:

on line 529

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