iterating nodes example 'char const*' error

Question

[Haluk]

Hi,

I'm following the provided code snippet of iterating nodes, but I got the terminate called after throwing an instance of 'char const*' error for the fasta test file in the link below.

[Ram]

What are you trying to do and which software are you using? You've added a gatb tag but said nothing about it on the post. Please, elaborate.

[Haluk]

Here is the code snippet provided in the GATB API Documentation.

I have the HDF5 file which is also generated by GATB. However, when I use the HDF5 file as an input to the program in the above, it gave me terminate called after throwing an instance of 'char const* error.

Answer 1

[Haluk]

It worked when I add the -abundance-min 1 option.

[edrezen]

Indeed, you found out what happened. You need to have at least one node in the graph, so in your example, the default abundance threshold (3 by default) is too high for such a small example, ie. there is no 31-mer occuring 3 times in the fasta file.

We will probably change in gatb-core the kind of exception in the case there is no node in the graph (change "char const*" into Exception).

Another solution is NOT to throw an exception if there is no node in the graph, but it may be confusing for the user because the program would do nothing without any notification.