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fritzsedlazeck / SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
MIT License
13 stars 2 forks source link

Install problem while make #1

Closed LeileiCui closed 7 years ago

LeileiCui commented 7 years ago

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

fritzsedlazeck commented 7 years ago

Hi Leilei, thanks for letting me know. I have fixed the code. You will need to download it again. Let me know if something else pops up. Thanks Fritz

LeileiCui commented 7 years ago

Tks for this quick reply, Fritz! The SURVIVOR_ant could be installed perfectly now.

Moreover, I still remember your amazing presentation about several softwares for SV calling and merge in UCL, and I just wonder is that fine for you to share that slide with me for further learning?

Best, Leilei

fritzsedlazeck commented 7 years ago

Hi Leilei, I can send you some slides from the UCL talk. Ping me at: fritz.sedlazeck@gmail.com Thanks Fritz