Fragment file sometimes contain 9 fields

[Jakob Nissen]

The fragment file sometimes contain 9 fields, whereas only the first 7 are documented in the KMAspecification.pdf. This caused a script of mine to fail.

What are the last two columns?

[ptlcc]

When KMA is run without the “-1t1” flag it allows several hits per query sequence. To save diskspace the part of the query containing the hit is cut out, and the last two columns denote the cuts in the original query.

[Jakob Nissen]

Aha, thank you. I think it would be nice to document in the kmaspecification.pdf then

[ptlcc]

You are completely right, it has been added now.