vg constuct maf import: `aln.second.size() == aln_len'

[ChriKub]

Hi,

I am trying to import a maf file that was constructed using progressiveCactus and hal2maf into vg but it fails. The file has passed the validation with maftools mafValidator. The maf file can be downloaded here.

Thanks

hal2maf 15.2.hal 15.2.maf
vg construct -M 15.2.maf > 15.2.vg

vg: src/msa_converter.cpp:135: vg::MSAConverter::MSAConverter(std::istream&, std::__cxx11::string, size_t): Assertion `aln.second.size() == aln_len' failed.

Stack trace (most recent call last):
#10 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x4b9ce8, in _start
#9 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x113a5b9, in __libc_start_main
#8 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x113a3c5, in generic_start_main
#7 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x404ee6, in main
Source "src/main.cpp", line 61, in main [0x404ee6]
#6 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x7e4f97, in vg::subcommand::Subcommand::operator()(int, char**) const
| Source "src/subcommand/subcommand.cpp", line 72, in operator()
Source "/usr/include/c++/5/functional", line 2267, in operator() [0x7e4f97]
2264: {
2265: if (_M_empty())
2266: __throw_bad_function_call();
>2267: return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
2268: }
2269:
2270: #if __cpp_rtti
#5 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x81707c, in main_construct(int, char**)
Source "src/subcommand/construct_main.cpp", line 334, in main_construct [0x81707c]
#4 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0xab1002, in vg::MSAConverter::MSAConverter(std::istream&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, unsigned long)
Source "src/msa_converter.cpp", line 135, in MSAConverter [0xab1002]
#3 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x113df3d, in __assert_fail
#2 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x113deda, in __assert_fail_base
#1 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0x114acd9, in abort
#0 Object "/ebio/abt6_projects9/abt6_software/bin/vg/bin/vg", at 0xce3549, in raise
Source "../sysdeps/unix/sysv/linux/pt-raise.c", line 35, in raise [0xce3549]

[ChriKub]

@jeizenga Thanks for fixing it.