Index error if file is empty

[mlarjim]

Hi!
I am a big fan of parsnp. I was using v1.7.4 so I decided to update parsnp to v2.0.5. However, I get this error:

File "miniconda3/envs/parsnp2/bin/parsnp", line 969, in parse_input_files
    if hdr[0] != ">":
       ~~~^^^
IndexError: string index out of range

It is due to an empty file in my genomes directory, but older versions overcome this problem.
Thank you in advance

[bkille]

Hi @mlarjim

So sorry for the late reply. I'll make sure the next update of Parsnp (which I'll release within the next week or so) will automatically check for this.

In the meantime, if you should be able to get around this by running parsnp with --validate-input. That flag will throw out any input file which is empty or has invalid formatting. (It isn't turned on by default as it can lead to longer runtimes for very large inputs).