validate segfaults if path contains a non-existant node

[ASLeonard]

This is likely an obscure corner case that is hard to protect against, but may be useful. I'm not sure if it is the responsibility of odgi to gracefully tell people their graphs are malformed rather than crashing, but there is at least a partial issue here.

Running odgi validate on a gfa where the path includes a non-existant node causes a segfault.

S       1       A
S       2       C
S       3       T
S       4       G
L       1       +       2       +       0M
L       1       +       3       +       0M
L       2       +       4       +       0M
P       foo     1+,2+,4+        0M
P       bar     1+,5+   0M

Arguably, the description of the subcommand should tell the user the paths are not consistent with the graph (since no path can contain node 5 since node 5 doesn't exist). This currently only checks for consistency with L-lines assuming L-lines are already consistent with S-lines.

Interestingly, a gfa with a link line containing a non-existant node raises a "Floating point exception"

S       1       A
S       2       C
S       3       T
S       4       G
L       1       +       2       +       0M
L       1       +       3       +       0M
L       2       +       4       +       0M
L       2       +       5       +       0M
P       foo     1+,2+,4+        0M
P       bar     1+,3+   0M

This can be guarded against with some checks in src/gfa_to_handle.cpp, namely for edges here

odgi/src/gfa_to_handle.cpp

Lines 89 to 91 in 2151dd8

	handlegraph::handle_t a = graph->get_handle(stol(e.source_name) - id_increment, !e.source_orientation_forward);
	handlegraph::handle_t b = graph->get_handle(stol(e.sink_name) - id_increment, !e.sink_orientation_forward);
	graph->create_edge(a, b);

and presumably for paths here

odgi/src/gfa_to_handle.cpp

Lines 127 to 129 in 2151dd8

	graph->get_handle(id,
	// in gfak, true == +
	!p->gfak.orientations[i++]));

Unsurprisingly since the issue originates in the gfa loading, almost all subcommands segfault if the path contains a non-existant node.

Best,
Alex

[AndreaGuarracino]

@ASLeonard, thank you for breaking ODGI xD I've put a few polite checks in #591. Could you try to break it again?

[ASLeonard]

The changes handle all the bad files I had. And they print a very useful message for the error as well!