fritzsedlazeck / survivor_ant Goto Github PK

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)

License: MIT License

CMake 0.43% C 20.95% C++ 24.78% Makefile 5.40% Shell 1.40% M4 0.10% HTML 38.51% CSS 0.20% SAS 0.04% CLIPS 0.10% Pascal 1.37% Ada 1.74% Assembly 2.76% C# 1.09% Batchfile 0.01% DIGITAL Command Language 0.53% Module Management System 0.03% Perl 0.08% Roff 0.08% Objective-C 0.42%

structural-variations annotation vcf svs

survivor_ant's People

Stargazers

Watchers

Forkers

alenzhao scalavision

survivor_ant's Issues

cmake error during installation: could not find OpenMP

missing some overlaps

Current version has a bug and is missing some overlaps. I will try to fix this in January.

installation error

Hello,

Thanks for sharing this software. Looking great for the annotation of structural variants.
I am hoping to try it but encountered the error while installing it.
Could you kindly look into this?

Best,
Jungmin

[jc2545@c13n01 build]$ make
Scanning dependencies of target zlibstatic
[  3%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.o
[  6%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/compress.o
[ 10%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/crc32.o
[ 13%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.o
[ 16%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzclose.o
[ 20%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzlib.o
[ 23%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzread.o
[ 26%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 30%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inflate.o
[ 33%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/infback.o
[ 36%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inftrees.o
[ 40%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inffast.o
[ 43%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.o
[ 46%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/uncompr.o
[ 50%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/zutil.o
[ 53%] Linking C static library libz.a
[ 53%] Built target zlibstatic
Scanning dependencies of target survivor_ant
[ 56%] Building CXX object src/CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o
[ 60%] Building CXX object src/CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o
[ 63%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o
[ 66%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/GFFParser.cpp.o
[ 70%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o
[ 73%] Building CXX object src/CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o
[ 76%] Linking CXX executable ../../bin/survivor_ant-core-0.1.0/survivor_ant
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::overlap(position_str, position_str, short, SVS_Node*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::insert(position_str, position_str, short, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, bool, TNode*&): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o:IntervallTree.cpp:function IntervallTree::inorder_addanno(position_str, position_str, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, TNode*, TNode*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::spacePrint(std::ostream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, int) const [clone .constprop.189]: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*) [clone .constprop.187]: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*) [clone .constprop.186]: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::HelpVisitor::~HelpVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::VersionVisitor::~VersionVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::IgnoreRestVisitor::~IgnoreRestVisitor(): error: undefined reference to 'operator delete(void*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::operator==(TCLAP::Arg const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::ArgException::what() const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::trimFlag(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: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::SwitchArg::combinedSwitchesMatch(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::add(TCLAP::Arg*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::substr(unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::CmdLine::missingArgsException(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::assign(char const*)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::longID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::longID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::shortID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::Arg::Arg(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&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, TCLAP::Visitor*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_shortUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function TCLAP::StdOutput::_longUsage(TCLAP::CmdLineInterface&, std::ostream&) const: error: undefined reference to 'std::__throw_out_of_range_fmt(char const*, ...)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function Parameter::parse_intput(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()'
CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o:SURVIVOR_ant.cpp:function void TCLAP::ExtractValue<int>(int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, TCLAP::ValueLike): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o:BEDParser.cpp:function BEDParser::parse_bed(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/GFFParser.cpp.o:GFFParser.cpp:function GFFParser::parse_gff(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::parse_stop(char const*): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::assign_lines(std::vector<SVS_Node*, std::allocator<SVS_Node*> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o:VCFParser.cpp:function VCFParser::parse_entries(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
/ycga-gpfs/apps/hpc/software/binutils/2.27-GCCcore-6.3.0/bin/ld.gold: the vtable symbol may be undefined because the class is missing its key function
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_info[abi:cxx11](SVS_Node*, std::pair<int, int>&): error: undefined reference to 'std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o:VCFPrinter.cpp:function VCFPrinter::print_entry(SVS_Node*, int, std::pair<int, int>&): error: undefined reference to 'std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
collect2: error: ld returned 1 exit status
make[2]: *** [../bin/survivor_ant-core-0.1.0/survivor_ant] Error 1
make[1]: *** [src/CMakeFiles/survivor_ant.dir/all] Error 2
make: *** [all] Error 2

Unexpected behaviour with gzipped gff

Hi Fritz,

I found another tool of you which looks useful... so here I am :)

When I annotate using a gzipped gff I get (quickly) the following output:

INITIALIZE VCF: 
Parse VCF: 0
Parse BED: 0
Parse GFF: 1
PRint: 
start printing
print entries 
Successfully finished
total entries: 651
overlapping vcf entries: 0
overlapping annotations: 649

But the resulting vcf only contains total_Annotations=0 for every line.

Using the same gff, but no longer compressed takes a bit longer and gives the following output:

INITIALIZE VCF: 
Parse VCF: 0
Parse BED: 0
Parse GFF: 1
PRint: 
start printing
print entries 
Successfully finished
total entries: 651
overlapping vcf entries: 0
overlapping annotations: 360

And this time the resulting vcf looks as expected, e.g.:
;total_Annotations=16;overlapped_Annotations=gene38311,rna81866,id909513,id909514,cds63851,cds63851,rna81870,

So this was surprising.

Am I right that from the gff the "ID" attribute is taken?

Cheers,
Wouter

cmake error during installation: could not find OpenMP

Hi,

I have followed the instructions to install SURVIVOR_ant on my laptop mac book pro. I got an error after 'cmake ..' that says it could not find OpenMP. I don't know what this is. I looked around on the web to see if I could find an answer but I could not make them work for me. I made sure I have 'open-mpi' installed with brew. I could not find the 'clang-omp' formula in brew. Can you help me, please?

cmake ..
-- The C compiler identification is AppleClang 9.0.0.9000039
-- The CXX compiler identification is AppleClang 9.0.0.9000039
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- No build type specified. Using 'release'
-- Try OpenMP C flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
Call Stack (most recent call first):
  /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
  /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindOpenMP.cmake:316 (find_package_handle_standard_args)
  CMakeLists.txt:23 (FIND_PACKAGE)


-- Configuring incomplete, errors occurred!
See also "/Users/user/Documents/project/output/software/SURVIVOR/build/CMakeFiles/CMakeOutput.log".
See also "/Users/user/Documents/project/output/software/SURVIVOR/build/CMakeFiles/CMakeError.log".

annotation in animal

In attempting to use SURVIVOR_ant in chicken annotation. I provided the GFF(Gallus_gallus.GRCg6a.98.gff3.gz) file VCF(gallus_gallus.vcf.gz) file and bed file(galGal6_ens_whole_gene.bed) from ensemblorg(http://asia.ensembl.org/info/data/ftp/index.html), Pcabio data sequencing alignment and SV detection by ngmlr and sniffles ,the calculation was completed quickly and no error was reported,but the gene in the annotation result is different from the gene in the GFF file, for example, GFF :ENSGALG00000001964 is located on chromosome 17, but the annotated VCF file shows that it is located on chromosome 7.The log file did not report an error, I do not know where there is a problem, this makes me confused.

SV type aware annotations?

Is SURVIVOR_ant aware of the SV type (ins, del, dup, tra, etc) when annotating variants?

In our experiment, we provided a VCF file with different SV types (merged from multiple samples with SURVIVOR) and a BED file with only inversions from the 1K genome project. All variants that overlapped the inversions (independently of their type) were annotated. The entries in the BED file look like this one:

1 10296138 10296749 INV:CINV_delly_INV00000621:CINV_delly:0.00039936

We are thinking of splitting our VCF into each SV type, annotate separately, and then merge, but we were hoping SURVIVOR_ant could take care of it!

Segfaults with some VCF files

In attempting to use SURVIVOR_ant, we encountered segfaults when using VCFs from DELLY, Breakseq or MetaSV. The manta VCF files appear to be handled correctly.

The command below will segfault:
survivor_ant-core-0.1.0 -i DELLY_combined.vcf -v metasv.vcf,diploid_manta.vcf,somatic_manta.vcf -o colo_test.vcf

The problem appears to be in TNode.h::add called by IntervallTree::add_vcf

VCF files:
(Added .txt extension to VCF files to allow upload)

DELLY_combined.vcf.txt
metasv.vcf.txt
diploid_manta.vcf.txt
somatic_manta.vcf.txt

Install problem while make

Hi, Fritz!

Tks for this nice software, just met a problem when I tried to "make", any suggestions about it?

....
Linking C static library libz.a
[ 55%] Built target zlibstatic
Scanning dependencies of target survivor_ant
[ 59%] Building CXX object src/CMakeFiles/survivor_ant.dir/tree/IntervallTree.cpp.o
[ 62%] Building CXX object src/CMakeFiles/survivor_ant.dir/SURVIVOR_ant.cpp.o
[ 66%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/BEDParser.cpp.o
[ 70%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/GFFParser.cpp.o
[ 74%] Building CXX object src/CMakeFiles/survivor_ant.dir/Parser/VCFParser.cpp.o
[ 77%] Building CXX object src/CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o
In file included from bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:8:
bin/11-SURVIVOR_ant/src/print/VCFPrinter.h: In member function 'void VCFPrinter::close_file()':
bin/11-SURVIVOR_ant/src/print/VCFPrinter.h:38: error: 'fclose' was not declared in this scope
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp: In member function 'void VCFPrinter::print_header(std::string)':
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:45: error: 'fprintf' was not declared in this scope
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp: In member function 'void VCFPrinter::init()':
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:98: error: 'fopen' was not declared in this scope
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp: In member function 'void VCFPrinter::print_orig_entry(SVS_Node*, int, std::pair<int, int>&)':
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:176: error: 'fprintf' was not declared in this scope
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:184: error: 'fprintf' was not declared in this scope
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp: In member function 'void VCFPrinter::print_entry(SVS_Node*, int, std::pair<int, int>&)':
bin/11-SURVIVOR_ant/src/print/VCFPrinter.cpp:274: error: 'fprintf' was not declared in this scope
make[2]: *** [src/CMakeFiles/survivor_ant.dir/print/VCFPrinter.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/survivor_ant.dir/all] Error 2
make: *** [all] Error 2

Best,
Leilei

annotation error

when I use SURVIVOR_ant for vcf file containing BND detected by pbsv.
for example:
the annotation for
"pbsv.BND.scaffoldA09:61716239-scaffoldA07:3695888"
is
"total_Annotations=2;overlapped_Annotations=BnaC09T0514400ZS.exon5,cds.BnaC09T0514400ZS"

the vcf file shows translocation is from A09 to A07, why the annotation shows the translocation is related to C09? and there are too many errors like this in the annotation file for BND, but I didn't find this problem in annotation file for INS、DEL、DUP.

unknown error

Code:

vcf1=Lumpy.vcf
vcf2=Delly.vcf
vcf3=Manta.vcf

$SurvivorPath/survivor_ant \

-o combined.vcf
-l 20
-v $vcf3 $vcf2 $vcf1
-i $vcf1
-b $hg19_geneANT

Output: PARSE ERROR: Argument: Delly.vcf
Couldn't find match for argument

The error info is two ambiguous to understand.

Thanks

Segmentation fault while annotating with a gff

Good afternoon,

I am trying to annotate and compare 2 SV callsets (2 identical mice : 1 with a disease and the other healthy). I have merged the two vcf files with survivor and and I wanted to annotate the resulting file with a gff file. Nevertheless I encountered a segmentation fault and I don't know how to resolve it.

This is what I get :

$ ../../scripts/SURVIVOR_ant/bin/survivor_ant-core-0.1.0/survivor_ant -i sample_merged.vcf -g ../Mus_musculus.GRCm38.96_cleaned.gff3 
INITIALIZE VCF: 
Parse VCF: 0
Parse BED: 0
Parse GFF: 1
PRint: 
start printing
print entries 
Segmentation fault

If you have any idea on how to improve please let me know,
Thank you for your time,

Madeleine

Looking for a good .bed or .gff annonation file for hg19

Hi Guys,
I am having difficulty looking for a usable annotation files. Could anyone share?

Thanks

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.

Jobs

Jooble