Segmentation fault

[jnalanko]

Hi, I'm getting this Segmentation fault. Am I doing something stupid or is it a bug?

./build/build test.fa 31 13 -o ./index/out.sshash

k = 31, m = 13, seed = 1, l = 6, c = 3, canonical_parsing = false, weighted = false
reading file 'test.fa'...
m_buffer_size 29411764
sorting buffer...
saving to file './sshash.tmp.run_1653987257158295118.minimizers.0.bin'...
read 1 sequences, 63 bases, 33 kmers
num_kmers 33
num_super_kmers 4
num_pieces 2 (+3.63636 [bits/kmer])
=== step 1: 'parse_file' 7.9e-05 [sec] (2393.94 [ns/kmer])
Segmentation fault

This is the file test.fna (I had to change the extension to .txt for github because github did not allow .fa file extension).

test.txt

[jermp]

Hi, yes I can confirm the segfault also on my end.
I'm looking into this now. Thank you for reporting!
(Have you tried also the other test files in /data? They work correctly for me.)

Anyway, it seems a problem with the ext-mem construction (latest commit).
I tried the commit before release 2.0.1 (c48948c)
and everything worked.
Can you confirm this?

[jnalanko]

I can confirm that data/unitigs_stitched/ecoli1_k31_ust.fa.gz works in the latest commit, and commit c48948c works for the file that caused the segfault.

[jermp]

Yeah, it's some silly corner cases for tiny files where a tmp file results empty.
I'm fixing this now and will let you know.

[jermp]

As of latest commit (480f1da), it should be fixed.
I can confirm it works on my end.
Can you check? Thanks!

[jnalanko]

Yes it works now, thanks!

[jermp]

Ok, I'm closing this.