Why is the not primary alignment flag set for some reads in the output file?

[Kathleen Tibbetts]

Hi,

We are trying out bsmap and have noticed that the "not primary
alignment" flag is set in the output SAM file for some reads, when it
is the only alignment for that read -- that is, there is no other
alignment that's the primary one. Can you tell us under what
circumstances this happens?

Thank you very much.

Kathleen