g-ram index of the reference sequence

[zakieh-tayyebi]

I am trying to do something similar to Simple Read Mapping.
But it takes too long, so I was wondering:
1- does the find function search for the patterns in parallel as default?
2- how can I index the reference sequence as well? for example, can I have a q-gram index of the reference and a q-gram index of the reads, and then map the reads to the reference?
3- by lowering the value of EPSILON, more positions would be discarded faster. so I think it should make the search faster. but that's not the case for me!?

[smehringer]

Hi @ztayyebi-wcm,

thanks for using SeqAn.
I hope @cpockrandt or @eseiler, who are more familiar with the find/index module, can help you out.

[smehringer]

@cpockrandt Ping!

[smehringer]

@eseiler ping

[h-2]

What is the status here?