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This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species.

License: MIT License

C++ 87.46% CMake 0.77% Python 7.73% C 1.32% Perl 0.30% Makefile 0.94% Shell 0.72% M4 0.43% R 0.04% Starlark 0.30%
pseudo-genome-sequence liftover gff variant-records gene-structure annotations transformation

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sunqiangzai tw7649116 qiushili bingou shenweima guoshuai1314 illarionovaanastasia

gean's Issues

make failed

Hi, baoxingsong!

I failed in compiling with the following error message.

$ make
-- Configuring done
-- Generating done
-- Build files have been written to: /home/lizz/software/GEAN
[  2%] Built target gtest
[  4%] Built target gtest_main
[  5%] Building CXX object CMakeFiles/gean.dir/src/impl/geneSyntenic.cpp.o
In file included from /home/lizz/software/GEAN/src/impl/../model/model.h:41:0,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/home/lizz/software/GEAN/src/impl/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
 //    uint32_t getQueryMiddlePos() const;\
 ^
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void myOrthologPairsSort(std::vector<OrthologPair>&, const double&, const double&, const double&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:25:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int idx=0;  idx<pairedSimilarFragments.size(); ++idx){
                      ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:29:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for( int jdx=idx; jdx< pairedSimilarFragments.size(); ++jdx ){
                               ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void longestPath(std::vector<OrthologPair>&, std::vector<OrthologPair>&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:148:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int idx = 1; idx < pairedSimilarFragments.size(); ++idx) {
                       ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void generateLongestOutput(const string&, const string&, const string&, const string&, const int&, double, double, double, const bool&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const double&, const double&, const double&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:377:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for( int i=0; i< it1->second.size(); ++i ){
                           ~^~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:388:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for(  int index=0; index<it1->second[i].getTranscripts().size(); ++index ){
                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:459:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for(  int index=0; index<g.getTranscripts().size(); ++index ){
                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cassert:44:0,
                 from /home/lizz/software/GEAN/src/impl/../model/variant.h:31,
                 from /home/lizz/software/GEAN/src/impl/../model/FirstLastList.h:32,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:29,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void longestPathQuota(std::vector<OrthologPair2>, std::vector<std::vector<OrthologPair2> >&, const bool&, double&, double&, double&, const int&, int&, int&, std::map<std::__cxx11::basic_string<char>, int>&, std::map<std::__cxx11::basic_string<char>, int>&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:676:53: error: call of overloaded ‘abs(double)’ is ambiguous
                 assert(abs(subMaxScore-high[i].score)<0.01);
                                                     ^
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:75:0,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/ext/string_conversions.h:41,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/bits/basic_string.h:5402,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/string:52,
                 from /home/lizz/software/GEAN/src/impl/../model/GenomeBasicFeature.h:27,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:27,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/usr/include/stdlib.h:770:12: note: candidate: int abs(int)
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/ext/string_conversions.h:41:0,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/bits/basic_string.h:5402,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/string:52,
                 from /home/lizz/software/GEAN/src/impl/../model/GenomeBasicFeature.h:27,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:27,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:185:3: note: candidate: __int128 std::abs(__int128)
   abs(__GLIBCXX_TYPE_INT_N_0 __x) { return __x >= 0 ? __x : -__x; }
   ^~~
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:180:3: note: candidate: long long int std::abs(long long int)
   abs(long long __x) { return __builtin_llabs (__x); }
   ^~~
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:172:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void generateLongestQuotaOutput(const string&, const string&, const string&, const string&, const int&, const bool&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const double&, const double&, const double&, double&, double&, double&, int&, int&, int&, const bool&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:783:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int id=0; id < it->second.size(); ++id ){
                        ~~~^~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:797:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for( int i=0; i< it1->second.size(); ++i ){
                           ~^~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:804:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for(  int index=0; index<it1->second[i].getTranscripts().size(); ++index ){
                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:897:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int index = 0; index < g.getTranscripts().size(); ++index) {
                                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cassert:44:0,
                 from /home/lizz/software/GEAN/src/impl/../model/variant.h:31,
                 from /home/lizz/software/GEAN/src/impl/../model/FirstLastList.h:32,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:29,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void chainer(std::vector<Score_t>, std::vector<std::vector<Score_t> >&, const int&, const int&, const double&, const double&, const double&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1105:61: error: call of overloaded ‘abs(double)’ is ambiguous
                         assert(abs(subMaxScore-high[i].score)<0.01);
                                                             ^
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:75:0,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/ext/string_conversions.h:41,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/bits/basic_string.h:5402,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/string:52,
                 from /home/lizz/software/GEAN/src/impl/../model/GenomeBasicFeature.h:27,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:27,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/usr/include/stdlib.h:770:12: note: candidate: int abs(int)
 extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
            ^~~
In file included from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/ext/string_conversions.h:41:0,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/bits/basic_string.h:5402,
                 from /home/lizz/anaconda2/envs/gcc6/gcc/include/c++/string:52,
                 from /home/lizz/software/GEAN/src/impl/../model/GenomeBasicFeature.h:27,
                 from /home/lizz/software/GEAN/src/impl/../model/model.h:27,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.h:8,
                 from /home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:5:
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:185:3: note: candidate: __int128 std::abs(__int128)
   abs(__GLIBCXX_TYPE_INT_N_0 __x) { return __x >= 0 ? __x : -__x; }
   ^~~
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:180:3: note: candidate: long long int std::abs(long long int)
   abs(long long __x) { return __builtin_llabs (__x); }
   ^~~
/home/lizz/anaconda2/envs/gcc6/gcc/include/c++/cstdlib:172:3: note: candidate: long int std::abs(long int)
   abs(long __i) { return __builtin_labs(__i); }
   ^~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp: In function ‘void generateDagChainerOutput(const string&, const string&, const string&, const string&, const int&, const bool&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, const double&, const double&, const double&, int, int, double, double, double, const bool&, const bool&)’:
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1182:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for( int id=0; id < it->second.size(); ++id ){
                        ~~~^~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1211:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for( i=0; i< it1->second.size(); ++i ){
                       ~^~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1215:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for(  int index=0; index<it1->second[i].getTranscripts().size(); ++index ){
                                        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1334:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (i = 0; i < it1->second.size(); ++i) {
                             ~~^~~~~~~~~~~~~~~~~~~~
/home/lizz/software/GEAN/src/impl/geneSyntenic.cpp:1337:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     for (int index = 0; index < g.getTranscripts().size(); ++index) {
                                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/gean.dir/src/impl/geneSyntenic.cpp.o] Error 1
make[1]: *** [CMakeFiles/gean.dir/all] Error 2
make: *** [all] Error 2

I am usingn gcc (GCC) 6.1.0 and cmake version 3.16.2.

Thanks for your help!

Build error

Build failed after 100% on Ubuntu 18.04.3 using GCC version 7.4.0

Error code is as follows:

[ 98%] Building CXX object CMakeFiles/gean.dir/src/impl/outPutORFConserveredTranscripts.cpp.o
In file included from /home/auxie001/GEAN/src/impl/../model/model.h:41:0,
from /home/auxie001/GEAN/src/impl/outPutORFConserveredTranscripts.h:8,
from /home/auxie001/GEAN/src/impl/outPutORFConserveredTranscripts.cpp:5:
/home/auxie001/GEAN/src/impl/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
// uint32_t getQueryMiddlePos() const;
^
/home/auxie001/GEAN/src/impl/outPutORFConserveredTranscripts.cpp: In function ‘void outPutORFConserveredTranscripts(const string&, const string&, const string&, const int&, std::map<std::__cxx11::basic_string, std::__cxx11::basic_string >&)’:
/home/auxie001/GEAN/src/impl/outPutORFConserveredTranscripts.cpp:27:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int index = 0; index < gene.getTranscripts().size(); ++index) {
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable gean
CMakeFiles/gean.dir/src/myImportandFunction/alignNeedlemanForTranscript_simd_avx2int32.cpp.o: In function checkElements(int const&, int const&, std::vector<SpliceSitePosition, std::allocator<SpliceSitePosition> > const&, int const&)': /home/auxie001/GEAN/src/myImportandFunction/alignNeedlemanForTranscript_simd_avx2int32.cpp:35: multiple definition of checkElements(int const&, int const&, std::vector<SpliceSitePosition, std::allocator > const&, int const&)'
CMakeFiles/gean.dir/src/myImportandFunction/alignNeedlemanForTranscript.cpp.o:/home/auxie001/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:394: first defined here
collect2: error: ld returned 1 exit status
CMakeFiles/gean.dir/build.make:2229: recipe for target 'gean' failed
make[2]: *** [gean] Error 1
CMakeFiles/Makefile2:68: recipe for target 'CMakeFiles/gean.dir/all' failed
make[1]: *** [CMakeFiles/gean.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2

transgff

Dear boiaxingsong,

I am trying to use the transgff function, but I cannot seem to find the right input for the -a similar segments option. I cannot get it to run without it. I tried using a sam output allignment between the two genomes between I am trying to transfer the genomen, but it is not working. I am trying to liftover the annotation from a previous version of the genome to a new version.

I hope you can help me.

Best wishes,
Sabine

error 

 cmake CMakeLists.txt
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /root/software/anaconda3/bin/python (found version "3.6.3") 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Configuring done
-- Generating done
-- Build files have been written to: /root/software/GEAN
[root@b5eb0c76b4dc GEAN]# ls
CMakeCache.txt  CMakeLists.txt  Makefile   SpliceSites          configure  example  googletest  script    src
CMakeFiles      LICENSE         README.md  cmake_install.cmake  doc        gean     main.cpp    song.cpp  updateLog
[root@b5eb0c76b4dc GEAN]# make
Scanning dependencies of target gtest
[  1%] Building CXX object googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[  2%] Linking CXX static library libgtest.a
[  2%] Built target gtest
Scanning dependencies of target gtest_main
[  3%] Building CXX object googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[  4%] Linking CXX static library libgtest_main.a
[  4%] Built target gtest_main
Scanning dependencies of target gean
[  5%] Building CXX object CMakeFiles/gean.dir/src/myImportandFunction/alignNeedlemanForTranscript.cpp.o
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp: In constructor 'NeedlemanWunschForTranscript::NeedlemanWunschForTranscript(std::string&, std::string&, int&, int&, std::vector<SpliceSitePosition>&, std::map<std::basic_string<char>, std::basic_string<char> >&, NucleotideCodeSubstitutionMatrix&)':
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:73:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < (this->_length_of_q + 1); i++) {
                                                ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:76:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i<= _length_of_q; i++) {
                         ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:81:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int j = 0; j<= _length_of_d; j++){
                         ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:90:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < (this->_length_of_q + 1); i++) {
                                                ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:95:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j <= _length_of_d; j++) {
                              ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:100:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i <= _length_of_q; i++) {
                              ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp: In destructor 'NeedlemanWunschForTranscript::~NeedlemanWunschForTranscript()':
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:110:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i <= _length_of_q; i++) {
                          ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp: In member function 'void NeedlemanWunschForTranscript::calculate_similarity(NucleotideCodeSubstitutionMatrix&)':
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:146:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int j=1; j < _length_of_d + 1; ++j){
                                      ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:148:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (i = 1; i < _length_of_q + 1; ++i) {
                                            ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:167:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (i = 1; i < _length_of_q + 1; ++i) {
                                            ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:186:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for ( i = 1; i < _length_of_q + 1; ++i) {
                                             ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:253:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (i = 1; i < _length_of_q + 1; ++i) {
                                            ^
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp: In member function 'void NeedlemanWunschForTranscript::get_optimal_alignment()':
/root/software/GEAN/src/myImportandFunction/alignNeedlemanForTranscript.cpp:333:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( k=_length_of_q; k>i; --k ){
                            ^
[  6%] Building CXX object CMakeFiles/gean.dir/src/myImportandFunction/alignNeedlemanWunsch_v2.cpp.o
[  8%] Building CXX object CMakeFiles/gean.dir/src/model/GenomeBasicFeature.cpp.o
[  9%] Building CXX object CMakeFiles/gean.dir/src/controlLayer.cpp.o
In file included from /root/software/GEAN/src/./util/../model/model.h:41:0,
                 from /root/software/GEAN/src/./util/myutil.h:25,
                 from /root/software/GEAN/src/./util/util.h:27,
                 from /root/software/GEAN/src/controlLayer.h:30,
                 from /root/software/GEAN/src/controlLayer.cpp:25:
/root/software/GEAN/src/./util/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
 //    uint32_t getQueryMiddlePos() const;\
 ^
[ 10%] Building CXX object CMakeFiles/gean.dir/src/InputParser.cpp.o
[ 11%] Building CXX object CMakeFiles/gean.dir/src/util/myutil.cpp.o
In file included from /root/software/GEAN/src/util/../model/model.h:41:0,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/myutil.cpp:26:
/root/software/GEAN/src/util/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
 //    uint32_t getQueryMiddlePos() const;\
 ^
[ 12%] Building CXX object CMakeFiles/gean.dir/src/util/nucleotideCodeSubstitutionMatrix.cpp.o
In file included from /root/software/GEAN/src/util/../model/model.h:41:0,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/nucleotideCodeSubstitutionMatrix.cpp:30:
/root/software/GEAN/src/util/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
 //    uint32_t getQueryMiddlePos() const;\
 ^
[ 13%] Building CXX object CMakeFiles/gean.dir/src/util/parameters.cpp.o
In file included from /root/software/GEAN/src/util/../model/model.h:41:0,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/parameters.cpp:25:
/root/software/GEAN/src/util/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
 //    uint32_t getQueryMiddlePos() const;\
 ^
/root/software/GEAN/src/util/parameters.cpp: In function 'std::string getexepath(char**)':
/root/software/GEAN/src/util/parameters.cpp:139:91: error: no matching function for call to 'regex_replace(std::back_insert_iterator<std::basic_string<char> >, std::basic_string<char>::iterator, std::basic_string<char>::iterator, std::regex&, const char [1])'
         std::regex_replace(std::back_inserter(temp), exeFile.begin(), exeFile.end(), e, "");
                                                                                           ^
/root/software/GEAN/src/util/parameters.cpp:139:91: note: candidates are:
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from /root/software/GEAN/src/util/../model/MsaFileRecord.h:41,
                 from /root/software/GEAN/src/util/../model/model.h:31,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/parameters.cpp:25:
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
/root/software/GEAN/src/util/parameters.cpp:139:91: note:   mismatched types 'const std::basic_string<_Ch_type>' and 'const char [1]'
         std::regex_replace(std::back_inserter(temp), exeFile.begin(), exeFile.end(), e, "");
                                                                                           ^
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from /root/software/GEAN/src/util/../model/MsaFileRecord.h:41,
                 from /root/software/GEAN/src/util/../model/model.h:31,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/parameters.cpp:25:
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
/root/software/GEAN/src/util/parameters.cpp:139:91: note:   'std::back_insert_iterator<std::basic_string<char> >' is not derived from 'const std::basic_string<_Ch_type>'
         std::regex_replace(std::back_inserter(temp), exeFile.begin(), exeFile.end(), e, "");
                                                                                           ^
/root/software/GEAN/src/util/parameters.cpp:145:89: error: no matching function for call to 'regex_replace(std::back_insert_iterator<std::basic_string<char> >, std::basic_string<char>::iterator, std::basic_string<char>::iterator, std::regex&, const char [1])'
     std::regex_replace(std::back_inserter(result), exeFile.begin(), exeFile.end(), e, "");
                                                                                         ^
/root/software/GEAN/src/util/parameters.cpp:145:89: note: candidates are:
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from /root/software/GEAN/src/util/../model/MsaFileRecord.h:41,
                 from /root/software/GEAN/src/util/../model/model.h:31,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/parameters.cpp:25:
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note: template<class _Out_iter, class _Bi_iter, class _Rx_traits, class _Ch_type> _Out_iter std::regex_replace(_Out_iter, _Bi_iter, _Bi_iter, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(_Out_iter __out, _Bi_iter __first, _Bi_iter __last,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2162:5: note:   template argument deduction/substitution failed:
/root/software/GEAN/src/util/parameters.cpp:145:89: note:   mismatched types 'const std::basic_string<_Ch_type>' and 'const char [1]'
     std::regex_replace(std::back_inserter(result), exeFile.begin(), exeFile.end(), e, "");
                                                                                         ^
In file included from /usr/include/c++/4.8.2/regex:62:0,
                 from /root/software/GEAN/src/util/../model/MsaFileRecord.h:41,
                 from /root/software/GEAN/src/util/../model/model.h:31,
                 from /root/software/GEAN/src/util/myutil.h:25,
                 from /root/software/GEAN/src/util/parameters.cpp:25:
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note: template<class _Rx_traits, class _Ch_type> std::basic_string<_Ch_type> std::regex_replace(const std::basic_string<_Ch_type>&, const std::basic_regex<_Ch_type, _Rx_traits>&, const std::basic_string<_Ch_type>&, std::regex_constants::match_flag_type)
     regex_replace(const basic_string<_Ch_type>& __s,
     ^
/usr/include/c++/4.8.2/bits/regex.h:2182:5: note:   template argument deduction/substitution failed:
/root/software/GEAN/src/util/parameters.cpp:145:89: note:   'std::back_insert_iterator<std::basic_string<char> >' is not derived from 'const std::basic_string<_Ch_type>'
     std::regex_replace(std::back_inserter(result), exeFile.begin(), exeFile.end(), e, "");
                                                                                         ^
make[2]: *** [CMakeFiles/gean.dir/src/util/parameters.cpp.o] Error 1
make[1]: *** [CMakeFiles/gean.dir/all] Error 2
make: *** [all] Error 2

gff2seq minimum intron size for ORF stats checking error

Hi Baoxing
In gean gff2seq:
when using argument:
-m INT minimum intron size for ORF stats checking
I tried different values, always getting error:

terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoi
Aborted (core dumped)

Elad

beta

AnnotationLiftOver V. beta

undefined reference to `clock_gettime'

[ 98%] Building CXX object CMakeFiles/gean.dir/src/impl/outPutORFConserveredTranscripts.cpp.o
In file included from /TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/../model/model.h:41:0,
from /TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/outPutORFConserveredTranscripts.h:8,
from /TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/outPutORFConserveredTranscripts.cpp:5:
/TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/../model/OrthologPair.h:53:1: warning: multi-line comment [-Wcomment]
// uint32_t getQueryMiddlePos() const;
^
/TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/outPutORFConserveredTranscripts.cpp: In function 'void outPutORFConserveredTranscripts(const string&, const string&, const string&, const int&, std::map<std::__cxx11::basic_string, std::__cxx11::basic_string >&)':
/TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/impl/outPutORFConserveredTranscripts.cpp:27:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int index = 0; index < gene.getTranscripts().size(); ++index) {
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable gean
/TJPROJ1/DENOVO/PROJ1/ceshi/likui/anaconda3/envs/3.72/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/gean.dir/src/util/parameters.cpp.o: in function generateUUID[abi:cxx11]()': /TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/util/../sole.h:454: undefined reference to clock_gettime'
/TJPROJ1/DENOVO/PROJ1/ceshi/likui/anaconda3/envs/3.72/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/gean.dir/src/util/parameters.cpp.o: in function generateUUID(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': /TJPROJ1/DENOVO/PROJ1/ceshi/likui/soft/GEAN/src/util/../sole.h:454: undefined reference to clock_gettime'
collect2: error: ld returned 1 exit status
make[2]: *** [gean] Error 1
make[1]: *** [CMakeFiles/gean.dir/all] Error 2
make: *** [all] Error 2

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