What is the difference between "maq match" and "maq map"

[cliff]

Hi, all

Does anyone know if "maq match" and "maq map" are the same thing?

From the reference page http://maq.sourceforge.net/maq-manpage.shtml, I found "maq map" is for mapping reads to the reference sequences. But on the maq manual http://maq.sourceforge.net/maq-man.shtml, it just says "maq match" is for mapping.

Which one should I use for mapping?

Thanks!

[jnfass]

same thing -- one's just an alias for the other (you'd have to ask Heng Li about the history of why there are two commands) ...