[Gatb-core-support] Problems with DBG construction in GATB

Leena Salmela leena.salmela at cs.helsinki.fi
Mar 21 Juil 12:58:42 CEST 2015


Dear GATB team,

First I would like to thank you for implementing a great library for 
sequence analysis. We have been using it for several projects of which 
LoRDEC and Gap2Seq (http://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq/) have 
been published.

Recently we have run into two problems when building DBGs:

1. If one tries to build two different DBGs on different read sets in the 
same program, GATB produces an error. Should this be possible?

2. In the case that there are no solid k-mers in the read set (but the 
read set is not empty either), GATB gives a segmentation fault. It would 
be more convenient if the construction would just throw an exception in 
this case.

Thank you very much & best regards,

Leena Salmela
Postdoctoral Researcher, D.Sc.(Tech)
leena.salmela at cs.helsinki.fi


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