vg construct fails on pbsv INS and DEL

[fbemm]

Please describe:

1. What you were trying to do

I am trying to construct a graph with INS and DEL from pbsv.

2. What you wanted to happen

That vg returns a graph.

3. What actually happened

Crash report for vg v1.16.0 "Rotondi"
Stack trace (most recent call last):
#9    Object "vg", at 0x4d6119, in _start
#8    Object "vg", at 0x19dce68, in __libc_start_main
#7    Object "vg", at 0x409a5a, in main
#6    Object "vg", at 0x9b8d57, in vg::subcommand::Subcommand::operator()(int, char**) const
#5    Object "vg", at 0x9ee08d, in main_construct(int, char**)
#4    Object "vg", at 0xe43779, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#3    Object "vg", at 0xe41ec7, in vg::Constructor::construct_graph(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#2    Object "vg", at 0xe3e681, in vg::Constructor::construct_chunk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<vcflib::Variant, std::allocator<vcflib::Variant> >, unsigned long) const
#1    Object "vg", at 0xed8ca5, in vcflib::Variant::parsedAlternates(bool, bool, bool, float, float, float, float, float, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
#0    Object "vg", at 0xeef57e, in CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)

4. What data and command line to use to make the problem recur, if applicable

vg construct -S -r ref.fasta -v ref.vcf > ref.vg

[glennhickey]

Sometimes adding a -f fixes these errors.

…

On Thu, May 23, 2019 at 9:09 AM Felix Bemm ***@***.***> wrote: Please describe: 1. What you were trying to do I am trying to construct a graph with INS and DEL from pbsv. 1. What you wanted to happen That vg returns a graph. 1. What actually happened Crash report for vg v1.16.0 "Rotondi" Stack trace (most recent call last): #9 Object "vg", at 0x4d6119, in _start #8 Object "vg", at 0x19dce68, in __libc_start_main #7 Object "vg", at 0x409a5a, in main #6 Object "vg", at 0x9b8d57, in vg::subcommand::Subcommand::operator()(int, char**) const #5 Object "vg", at 0x9ee08d, in main_construct(int, char**) #4 Object "vg", at 0xe43779, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>) #3 Object "vg", at 0xe41ec7, in vg::Constructor::construct_graph(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>) #2 Object "vg", at 0xe3e681, in vg::Constructor::construct_chunk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<vcflib::Variant, std::allocator<vcflib::Variant> >, unsigned long) const #1 Object "vg", at 0xed8ca5, in vcflib::Variant::parsedAlternates(bool, bool, bool, float, float, float, float, float, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) #0 Object "vg", at 0xeef57e, in CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) 1. What data and command line to use to make the problem recur, if applicable vg construct -S -r ref.fasta -v ref.vcf > ref.vg — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2278?email_source=notifications&email_token=AAG373RT7OXAWTMK7HJVTMDPW2JRNA5CNFSM4HPDTSNKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GVOU2IQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAG373QOF5MOXZB65L2J4GTPW2JRNANCNFSM4HPDTSNA> .

[fbemm]

Works! Thanks

[ekg]

We might want to make that the default for large variants.

…

On Thu, May 23, 2019, 16:15 Felix Bemm ***@***.***> wrote: Closed #2278 <#2278>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2278?email_source=notifications&email_token=AABDQEOFP7TMKDZR36CVLN3PW2RGZA5CNFSM4HPDTSNKYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGORTJMNSA#event-2362623688>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABDQELBAI7AZYXLFN7FJ5TPW2RGZANCNFSM4HPDTSNA> .

[egoltsman]

Just a heads up - I ran into this issue with the 1.28 build. I know vcf files can come in all sorts of weird shapes, and it's impossible to accommodate them all. What would help is if the program printed out the line that it couldn't parse. That, along with the stacktrace would give users some hints.

Thanks!