Question: iterating nodes example 'char const*' error
0
gravatar for Haluk
2.4 years ago by
Haluk160
Lincoln, Nebraska
Haluk160 wrote:

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.

gatb • 683 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Haluk160

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.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Ram12k

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.

ADD REPLYlink written 2.4 years ago by Haluk160
3
gravatar for Haluk
2.4 years ago by
Haluk160
Lincoln, Nebraska
Haluk160 wrote:

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

ADD COMMENTlink written 2.4 years ago by Haluk160
1

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.


 

ADD REPLYlink written 2.4 years ago by edrezen680
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