vg view on snarls protobuf file

1. What were you trying to do? I created a test pangenome with the Minigraph-Cactus pipeline using the provided yeast test data as follows:

singularity pull docker://quay.io/comparative-genomics-toolkit/cactus:v2.6.4-gpu
singularity exec cactus_v2.6.4-gpu.sif cactus-pangenome ./js ./examples/yeastPangenome.txt --reference S288C --outDir yeast-pg --outName yeast-pg --vcf --giraffe --gbz --gfa --odgi --chrom-vg --chrom-og --viz --draw

Then, I was looking into all files to what information they contained. When I got the the snarls file (yeast-pg/yeast-pg.snarls), I ran into problems. I tried the following:

vg view -jE yeast-pg/yeast-pg.snarls

2. What did you want to happen? See the contents of the snarls file in JSON format.

3. What actually happened?

terminate called after throwing an instance of 'std::runtime_error'
  what():  [io::ProtobufIterator] tag "SNARL" for Protobuf that should be "vg.SnarlTraversal"

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.49.0 "Peschici"
Stack trace (most recent call last):
#15   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x615534, in _start
#14   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x2056606, in __libc_start_main
#13   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x2054da9, in __libc_start_call_main
#12   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0xdf08ab, in vg::subcommand::Subcommand::operator()(int, char**) const
#11   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0xe6b7a9, in main_view(int, char**)
#10   Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x1421cb7, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#9    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0xe6c578, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#38}>::_M_invoke(std::_Any_data const&, std::istream&)
#8    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0xe6fa72, in void vg::io::for_each<vg::SnarlTraversal>(std::istream&, std::function<void (long, vg::SnarlTraversal&)> const&)
#7    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0xe6f8ef, in vg::io::ProtobufIterator<vg::SnarlTraversal>::fill_value()
#6    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x1f8ea98, in __cxa_throw
#5    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x1f8e936, in std::terminate()
#4    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x1f8e8cb, in __cxxabiv1::__terminate(void (*)())
#3    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x5e1c83, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#2    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x5e43cb, in abort
#1    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x206d7e5, in raise
#0    Object "/lustre/BIF/nobackup/worku005/bin/miniconda3/envs/bio/bin/vg", at 0x209a1ec, in __pthread_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!
━━━━━━━━━━━━━━━━━━━━

5. What data and command can the vg dev team use to make the problem happen? See the test data from the Minigraph-Cactus pipeline and the mentioned commands above.

6. What does running vg version say?

vg version v1.49.0 "Peschici"
Compiled with g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 on Linux
Linked against libstd++ 20220421
Built by anovak@octagon

vgteam / vg

vg view on snarls protobuf file #4026