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 

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 

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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