Differences between softclip and softclipOverhangs

[MarcelloMalpighi]

Hello,

I am currently using Salmon v1.10.3. According to https://combine-lab.github.io/salmon-tutorials/2021/softclip/, --softclipOverhangs should have the exact same effect as --softclip. However, I observe subtle differences when using each flag individually or in combination. I would greatly appreciate clarification on the differences between --softclip and --softclipOverhangs. Additionally, since --maxSoftclipFraction no longer appears to be available, could you please advise whether its behavior can be controlled using an alternative flag?

Thank you.