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:

RagTag/ragtag_scaffold.py

Line 528 in 11f670b

# Check if the gap size is too small or too large

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 — Reply to this email directly, view it on GitHub <#101 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXOL4W6D5L5TCEIUIWTEYLDUZ3Y6PANCNFSM5MWIY6UA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>