Update MitoGeneExtractor.cpp (v1.9.6 conflict merging unresolved error)

[SchistoDan]

Fix unresolved conflict merging that resulted in a make error when compiling:

**make MitoGeneExtractor-v1.9.6beta4**
g++ -O2 -std=c++11 -Wno-alloc-size-larger-than  -I . -I tclap-1.2.5/include  MitoGeneExtractor.cpp global-types-and-parameters_MitoGeneExtractor.cpp exonerate_wrapper_and_parser.cpp -o MitoGeneExtractor-v1.9.6
MitoGeneExtractor.cpp:1774:27: error: too many decimal points in number
 1774 | >>>>>>> refactor-bugfix-v1.9.6
      |                           ^~~~
MitoGeneExtractor.cpp: In function ‘int main(int, char**)’:
MitoGeneExtractor.cpp:1770:1: error: version control conflict marker in file
 1770 | <<<<<<< HEAD
      | ^~~~~~~
make: *** [makefile:21: MitoGeneExtractor-v1.9.6beta4] Error 1

Caused by the lines below (1770) in MitoGeneExtractor.cpp:

<<<<<<< HEAD
    cout << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: "
=======
    cerr << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: "
>>>>>>> refactor-bugfix-v1.9.6
    << seqs_DNA_reads_target.GetTaxaNum()  << endl;

Replacing the above with the following:

    cerr << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: "
    << seqs_DNA_reads_target.GetTaxaNum()  << endl;

And rerunning the make command resulted in succesful compilation.

[cmayer]

Hi Dan, I just fixed this issue. I have tested the refactor-bugfix-v1.9.6. During merging I had a few issues and I though that I had fixed them. I should have tested this again. I created a new release which fixed the issue. Best Christoph

Am 24.09.2025 um 11:55 schrieb Dan Parsons ***@***.***>: Fix unresolved conflict merging that resulted in a make error when compiling: **make MitoGeneExtractor-v1.9.6beta4** g++ -O2 -std=c++11 -Wno-alloc-size-larger-than -I . -I tclap-1.2.5/include MitoGeneExtractor.cpp global-types-and-parameters_MitoGeneExtractor.cpp exonerate_wrapper_and_parser.cpp -o MitoGeneExtractor-v1.9.6 MitoGeneExtractor.cpp:1774:27: error: too many decimal points in number 1774 | >>>>>>> refactor-bugfix-v1.9.6 | ^~~~ MitoGeneExtractor.cpp: In function ‘int main(int, char**)’: MitoGeneExtractor.cpp:1770:1: error: version control conflict marker in file 1770 | <<<<<<< HEAD | ^~~~~~~ make: *** [makefile:21: MitoGeneExtractor-v1.9.6beta4] Error 1 Caused by the lines below (1770) in MitoGeneExtractor.cpp: <<<<<<< HEAD cout << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: " ======= cerr << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: " >>>>>>> refactor-bugfix-v1.9.6 << seqs_DNA_reads_target.GetTaxaNum() << endl; Replacing the above with the following: cerr << "PROGRESS: Finished reading input DNA sequences. Found this number of input DNA sequences: " << seqs_DNA_reads_target.GetTaxaNum() << endl; And rerunning the make command resulted in succesful compilation. You can view, comment on, or merge this pull request online at: #18 <#18> Commit Summary 5db4168 <5db4168> Update MitoGeneExtractor.cpp File Changes (1 file <https://github.com/cmayer/MitoGeneExtractor/pull/18/files>) M MitoGeneExtractor.cpp <https://github.com/cmayer/MitoGeneExtractor/pull/18/files#diff-52f6bd7e5f0cc7d704f01b66d784d0ff607663fac5156e12303f1923a3f11eb3> (4) Patch Links: https://github.com/cmayer/MitoGeneExtractor/pull/18.patch <https://github.com/cmayer/MitoGeneExtractor/pull/18.patch> https://github.com/cmayer/MitoGeneExtractor/pull/18.diff <https://github.com/cmayer/MitoGeneExtractor/pull/18.diff> — Reply to this email directly, view it on GitHub <#18>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAPNDIFKZNLHLLNBTSUURJD3UJTCZAVCNFSM6AAAAACHLPAZPOVHI2DSMVQWIX3LMV43ASLTON2WKOZTGQ2DQNRTG44DKMI>. You are receiving this because you are subscribed to this thread.

**************************************** Dr. Christoph Mayer Email: ***@***.*** Tel.: +49 (0)228 9122 403 Head of the Section Statistical Phylogenetics & Phylogenomics Leibniz-Institut zur Analyse des Biodiversitätswandels (LIB), Standort Bonn, Zoologisches Forschungsmuseum Alexander Koenig Adenauerallee 127 53113 Bonn, Germany www.zfmk.de Stiftung des öffentlichen Rechts; Direktor: Prof. B. Misof Sitz: Bonn ****************************************