GATB - Bloom filter for k-mers

Question

[karel.brinda]

Hello,

I would like to use the GATB library for creating a Bloom filter for k-mers. Please, could you have a look on this code and recommend me what should I correct?

http://pastebin.com/8vgiTTjx

I am currently getting this error:

http://pastebin.com/MFWyWamx

Thanks!

Answer 1

[edrezen]

Hello,

The issue is indeed on line 19 when you try to insert an item in the Bloom filter.

Actually, the 'kmer' object (of class ModelDirect::Kmer) is not of type Type (which is only the numerical value of the kmer); it holds several methods, including an accessor value() to the actual numerical value of the kmer.

So, the correction of your code should be:

bloom->insert (kmer.value());

Can you tell me if it works?

[karel.brinda]

Great, it works. Thank you!!! Btw. it seems that the method contains for Bloom is not const. Is there any reason for it?

[edrezen]

You are welcome.

Thank you for your remark; actually there is no special reason why it is not const, and it wouldn't hurt to turn it const (maybe in a next release)