parsnpAligner.log sequence lengths discrepancies

[AbigailShockey]

Hello Parsnp devs,

I noticed that the sequence lengths reported in the parsnpAligner.log file do not match the actual sequence lengths of the fasta files provided to Parsnp. The values are larger than expected. How are these values calculated, and do these inflated sequence lengths affect the cluster coverages reported in the parsnpAligner.log file?

I've attached an example of a log file demonstrating this phenomenon. For this run, I used the -r ! option to randomly choose a reference. Sample1, which has a sequence length of 3987309 bps, was chosen as a reference. The sequence length was correctly reported for Sequence 1 (Sample1.fa.ref, line 3) but incorrectly reported as 4035049 bps for Sequence 6 (Sample1.fa, line 28). The other sequence lengths are also incorrectly reported.

I appreciate any assistance on this,

Best,
Abigail

parsnpAligner.log