just wondering if anyone else in Galaxy land was having this problem, I
emailed tophat.cufflinks@ to let them know
We have been experiencing segmentation faults with cufflinks 1.0.3. Our
platform is CentOS 5.5, and we compiled from source using gcc 4.1.2 (Red Hat
4.1.2-48).
The segmentation fault occured when we passed in a GTF annotation file with the
-G option. Using gdb, I tracked it down to line 218 in bundles.cpp:
string rs = (rna_seq) ? rna_seq:"";
It appeared that in our case rna_seq was uninitialized and did not point to a
valid C string.
char* rna_seq;
if (loadSeqs && faseq) {
rna_seq = rna.getSpliced(faseq, false, &seqlen);
}
...
if (loadSeqs) {
string rs = (rna_seq) ? rna_seq:"";
...
}
As you can see, it would be possible for the first if-block to not execute, but
the second one to still execute (loadSeqs = true, faseq = false). I tried
making the following change to the declaration of rna_seq to initialize it to
NULL:
char* rna_seq = 0;
this stopped the segmentation fault we were seeing
--
Glen L. Beane
Senior Software Engineer
The Jackson Laboratory
(207) 288-6153
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