Segmentation Fault (Core dumped)

[casparbein]

Thanks for developing this tool.
Just wanted to report that reading in a gzipped fastq file containing ~3.5 million reads with pyfastx v2.1.0 and v2.0.0 leads to an almost immediate error: Segmentation fault (core dumped). Downgrading to v1.1.0 solved the issue, as I did change nothing else in my code.

[lmdu]

Thanks for reporting this issue. I will fixed it in next version.

[chrisAta]

Hi, I encountered the same Segmentation Fault (Core dumped) issue with pyfastx version 2.2.2. I was trying to use a command like this:

import pathlib
import pyfastx

path_to_fasta = pathlib.Path("/some/path/seq.fasta")
fasta = pyfastx.Fasta(path_to_fasta, build_index=False)

where path_to_fasta was a Path object from pathlib. Converting it to a string works though:

import pathlib
import pyfastx

path_to_fasta = pathlib.Path("/some/path/seq.fasta")
fasta = pyfastx.Fasta(str(path_to_fasta), build_index=False)