FastGA crashes on fragmented assembly

[glennhickey]

Seems like a similar issue to #10. While it's understandable that FastGA may not align tiny contigs, it would be better if it could handle them without crashing if possible.

to reproduce:

wget -q https://public.gi.ucsc.edu/~hickey/debug/fastga-crash-2/Anc4_0.fa.gz
wget -q https://public.gi.ucsc.edu/~hickey/debug/fastga-crash-2/GCF_036013475.1-Columba_livia_0.fa.gz

FastGA  Anc4_0.fa.gz GCF_036013475.1-Columba_livia_0.fa.gz

fails with

FAtoGDB: Missing sequence entry at line 11074698 in file ./Anc4_0.fa.gz

FastGA: Call to FAtoGDB failed

thanks!

[c-zhou]

Hello Glenn,

The problem comes from a sequence of all 'n's (see below). We are on it and will let you know once it is fixed.

>id=Anc4|Anc4refChr313|100|0
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

Chenxi

[richarddurbin]

Of course FASTGA shouldn’t crash, but one could say that it is a bug to reconstruct an ancestral sequence that is all n’s. At any rate, this won’t align to anything. From: Chenxi Zhou ***@***.***> Date: Monday, 22 September 2025 at 17:54 To: thegenemyers/FASTGA ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [thegenemyers/FASTGA] FastGA crashes on fragmented assembly (Issue #18) [https://avatars.githubusercontent.com/u/11916266?s=20&v=4]c-zhou left a comment (thegenemyers/FASTGA#18)<#18 (comment)> Hello Glenn, The problem comes from a sequence of all 'n's (see below). We are on it and will let you know once it is fixed.

id=Anc4|Anc4refChr313|100|0

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