Hi,
this is Jose R Valverde, from CNB/CSIC in Spain.
I have run into a "bug" in the software that popped up while
running ldHgGene, and which resulted in the program crashing with a
segmentation violation while converting a data file from GFF to GenePred
format.
Using a debugger I could trace the problem to kent/src/lib/gff.c,
line 100, where the library makes use of the strcpy function which is
unsafe and, with this dataset, resulted in a buffer overrun of nameBuf.
The solution I used was to change
strcpy(nameBuf, groupName);
by
strncpy(nameBuf, groupName,511);
This allowed me to complete the run, but I am not sure -as I haven't
dwelt deeper in the code- if it is a good fix for, if groupName exceeds
nameBuf size and is truncated on output, it might do more harm than
good. My problem is the scarcity of documentation on the formats and
logic of the program, which would require me a long dive into the code
to find out, so if you could confirm and definitely fix the problem, I'd
be most grateful.
Sincerely.
jr
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