Hisat3n-table: unexpected strand info and missing sites?

[ZqF2017]

Hello,

Thank you for this wonderful tool.
We have a paired-end, stranded RNA-seq data with base change A -> G, and we used '--directional-mapping' during the alignment step.
As expected, the aligned reads are all tagged with "YZ:A:+" .

However, in the hisat3n-table output there are a few sites with strand as '-'.

Also, quite a few sites were NOT counted by hisat3n-table (red arrow), while they looked covered in IGV.

So our questions are:

1. Why are some sites reported with "-" strand?
2. Why are some sites omitted by hisat3n-table?

We are using version 2.2.1-3n-0.0.3.

Looking forward to hearing from you. Thanks in advance!