Segmentation fault with cyclic graph

[ldenti]

Hi,
I was trying to align reads to a cyclic graph with 8 self-loops (at least vg stats --is-acyclic --self-loops says so) but PanAligner crashed after loading the graph (segfault).

Here the data (data.tar.gz) and this is the command I'm using:

./PanAligner -cx lr graph.gfa reads.fq

This is the beginning and end of gdb backtrace:

#0  0x000000000044bd00 in std::_Bit_iterator::_Bit_iterator (this=0x7fffff7ff070, __x=0x1be4a0c0, __y=<error reading variable: Cannot access memory at address 0x7fffff7feffc>) at /usr/include/c++/11.2.0/bits/stl_bvector.h:243
#1  0x000000000045210a in std::vector<bool, std::allocator<bool> >::begin (this=0x7fffffffd430) at /usr/include/c++/11.2.0/bits/stl_bvector.h:832
#2  0x000000000044db3a in std::vector<bool, std::allocator<bool> >::operator[] (this=0x7fffffffd430, __n=74605) at /usr/include/c++/11.2.0/bits/stl_bvector.h:907
#3  0x000000000043d8c3 in Fillorder (un_adj=std::vector of length 535752, capacity 535752 = {...}, visited=std::vector<bool> of length 535752, capacity 535808 = {...}, u=74605, 
    stack=std::stack wrapping: std::deque with 23 elements = {...}) at graphUtils.cpp:15
#4  0x000000000043d96d in Fillorder (un_adj=std::vector of length 535752, capacity 535752 = {...}, visited=std::vector<bool> of length 535752, capacity 535808 = {...}, u=74604, 
    stack=std::stack wrapping: std::deque with 23 elements = {...}) at graphUtils.cpp:20
#5  0x000000000043d96d in Fillorder (un_adj=std::vector of length 535752, capacity 535752 = {...}, visited=std::vector<bool> of length 535752, capacity 535808 = {...}, u=74602, 
    stack=std::stack wrapping: std::deque with 23 elements = {...}) at graphUtils.cpp:20
...
#74831 0x000000000043d96d in Fillorder (un_adj=std::vector of length 535752, capacity 535752 = {...}, visited=std::vector<bool> of length 535752, capacity 535808 = {...}, u=1, stack=std::stack wrapping: std::deque with 23 elements = {...}) at graphUtils.cpp:20
#74832 0x000000000043d96d in Fillorder (un_adj=std::vector of length 535752, capacity 535752 = {...}, visited=std::vector<bool> of length 535752, capacity 535808 = {...}, u=0, stack=std::stack wrapping: std::deque with 23 elements = {...}) at graphUtils.cpp:20
#74833 0x000000000043df09 in SCC (adj=std::vector of length 535752, capacity 535752 = {...}, n_vtx=535752) at graphUtils.cpp:90
#74834 0x000000000044081f in graphUtils::Connected_components (this=0xb6e0710) at graphUtils.cpp:562
#74835 0x000000000042436c in mg_index (g=0x4b70a0, io=0x7fffffffdc34, n_threads=4, mo=0x7fffffffdab0) at index.c:243
#74836 0x000000000043716b in mg_map_files (g=0x4b70a0, n_fn=1, fn=0x7fffffffde78, ipt=0x7fffffffdc34, opt0=0x7fffffffdc40, n_threads=4) at gmap.c:192
#74837 0x00000000004726d1 in main (argc=5, argv=0x7fffffffde58) at main.c:293

Am I doing something wrong?

Thanks!

[ldenti]

Just saw issue #8 . So I suspect that this can be related to it since I'm not using a graph created with minigraph.