#16 MaqView --> MaqIndex 0.2.5 Segfaults

[Anonymous]

Maqindex in maqview 0.2.5 segfaults when indexing a map file in which any reference sequence has zero reads mapped to it. The segfault itself occurs in a call to fprintf in maqmap_index_main.c here:

assert(mi = make_map_index(argv[optind], level));
close_map_index(mi);
fprintf(stderr, "DONE!\n"); // <- Segfault

Commenting out this fprintf allows maqindex to complete without error, but the resulting index files inevitably cause maqview to crash at some later point, suggesting a buffer overflow or memory corruption within the call tree of make_map_index that leads to invalid index files in this case.

I would try to investigate further, but the code inside make_map_index is quite dense and uncommented...

I am using maqview on OS X 10.5 built as a 64-bit application. It works flawlessly if I remove reference sequences that have zero reads mapping to them, so I am quite confident that this is the triggering case.

Thanks, Vaughn

vsi@u.washington.edu