vg

[xiaoguizz]

1. What were you trying to do?

I would like to construct vg graph and map reads
2. What did you want to happen?
ERROR: Signal 6 occurred.

3. What actually happened?
vg: src/constructor.cpp:781: vg::ConstructedChunk vg::Constructor::construct_chunk(std::string, std::string, std::vectorvcflib::Variant, size_t) const: Assertion `last_edit_end != -1' failed.

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:

Place stacktrace here.

Crash report for vg v1.43.0 "Barisano"
Stack trace (most recent call last):
#12 Object "/share/home/zhouqinghong/software/vg", at 0x5e66ad, in _start
#11 Object "/share/home/zhouqinghong/software/vg", at 0x1e9622f, in __libc_start_main
#10 Object "/share/home/zhouqinghong/software/vg", at 0x5b63ae, in main
#9 Object "/share/home/zhouqinghong/software/vg", at 0xcf39fb, in vg::subcommand::Subcommand::operator()(int, char**) const
#8 Object "/share/home/zhouqinghong/software/vg", at 0xcaec96, in main_construct(int, char**)
#7 Object "/share/home/zhouqinghong/software/vg", at 0xdf9dc1, in vg::Constructor::construct_graph(std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::function<void (vg::Graph&)> const&)
#6 Object "/share/home/zhouqinghong/software/vg", at 0xdf90dd, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocatorvcflib::VariantCallFile* > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)> const&)
#5 Object "/share/home/zhouqinghong/software/vg", at 0xdf7c42, in vg::Constructor::construct_graph(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)> const&)
#4 Object "/share/home/zhouqinghong/software/vg", at 0xdf5184, in vg::Constructor::construct_chunk(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::vector<vcflib::Variant, std::allocatorvcflib::Variant >, unsigned long) const
#3 Object "/share/home/zhouqinghong/software/vg", at 0x1ea65d5, in __assert_fail
#2 Object "/share/home/zhouqinghong/software/vg", at 0x5b57a7, in __assert_fail_base.cold
#1 Object "/share/home/zhouqinghong/software/vg", at 0x5b58d7, in abort
#0 Object "/share/home/zhouqinghong/software/vg", at 0x14a0e4b, in raise

5. What data and command can the vg dev team use to make the problem happen?

vg construct -t 6 -S -a -f -r $ref -v $vars> test.vg
6. What does running vg version say?

Place vg version output here

vg: variation graph tool, version v1.43.0 "Barisano"