BOL: Installing NextSV on Ubuntu !

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Jit
Installing NextSV on Ubuntu !
Installing NextSV on Ubuntu !

By Jit 2091 days ago
➜  Tools git:(master) ✗ git clone https://github.com/Nextomics/nextsv.git 
Cloning into 'nextsv'...
remote: Counting objects: 369, done.
remote: Total 369 (delta 0), reused 0 (delta 0), pack-reused 369
Receiving objects: 100% (369/369), 51.81 MiB | 21.72 MiB/s, done.
Resolving deltas: 100% (223/223), done.
Checking connectivity... done.
➜  Tools git:(master) ✗ cd nextsv 
➜  nextsv git:(master) pip install argparse
Collecting argparse
  Downloading https://files.pythonhosted.org/packages/f2/94/3af39d34be01a24a6e65433d19e107099374224905f1e0cc6bbe1fd22a2f/argparse-1.4.0-py2.py3-none-any.whl
Installing collected packages: argparse
Successfully installed argparse-1.4.0
➜  nextsv git:(master) pip install pysam   
Requirement already satisfied: pysam in /home/urbe/anaconda3/lib/python3.6/site-packages (0.14.1)
➜  nextsv git:(master) pip install networkx
Requirement already satisfied: networkx in /home/urbe/anaconda3/lib/python3.6/site-packages (2.1)
Requirement already satisfied: decorator>=4.1.0 in /home/urbe/anaconda3/lib/python3.6/site-packages (from networkx) (4.3.0)
➜  nextsv git:(master) pip install h5py    
Requirement already satisfied: h5py in /home/urbe/anaconda3/lib/python3.6/site-packages (2.7.1)
Requirement already satisfied: numpy>=1.7 in /home/urbe/anaconda3/lib/python3.6/site-packages (from h5py) (1.14.3)
Requirement already satisfied: six in /home/urbe/anaconda3/lib/python3.6/site-packages (from h5py) (1.11.0)
➜  nextsv git:(master) pip install PyIntervalTree
Collecting PyIntervalTree
  Downloading https://files.pythonhosted.org/packages/aa/53/dbdb521c8e36301108114878ff1620255c559c12ba8fe0ce2eaf9b65cbef/PyIntervalTree-0.5.zip
Requirement already satisfied: sortedcontainers in /home/urbe/anaconda3/lib/python3.6/site-packages (from PyIntervalTree) (1.5.10)
Building wheels for collected packages: PyIntervalTree
  Running setup.py bdist_wheel for PyIntervalTree ... done
  Stored in directory: /home/urbe/.cache/pip/wheels/23/26/eb/83ac050fa1d31ed660d26a2508a47799728b29a9a0048a6b17
Successfully built PyIntervalTree
Installing collected packages: PyIntervalTree
Successfully installed PyIntervalTree-0.5
➜  nextsv git:(master) sh install_pbhoney.sh 
#### installation of PBHoney ####

########################################################################

Please add the following environmental variables to your ~/.bashrc file:

export SWEETPATH=/home/urbe/Tools/nextsv/aligners_and_callers/PBSuite_15.8.24
export PYTHONPATH=$PYTHONPATH:$SWEETPATH
export PATH=$PATH:$SWEETPATH/bin

########################################################################

➜  nextsv git:(master) ✗ sh install_sniffles.sh 
#### installation of Sniffles ####
building Sniffles
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- No build type specified. Using 'release'
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/build
Scanning dependencies of target zlibstatic
[  1%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.o
[  2%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/compress.o
[  3%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/crc32.o
[  4%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.o
[  5%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzclose.o
[  6%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzlib.o
[  7%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzread.o
[  8%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzwrite.o
[  9%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inflate.o
[ 10%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/infback.o
[ 11%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inftrees.o
[ 12%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inffast.o
[ 13%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.o
[ 14%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/uncompr.o
[ 15%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/zutil.o
[ 16%] Linking C static library libz.a
[ 16%] Built target zlibstatic
Scanning dependencies of target BamTools-static
[ 17%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[ 18%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[ 19%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
[ 20%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
[ 21%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
[ 22%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[ 23%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[ 24%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[ 25%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 26%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 27%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 28%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 29%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 30%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 31%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
[ 32%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
[ 34%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 35%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(
                          ^
[ 36%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
[ 37%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 38%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 39%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 40%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
                                                           ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
                                                           ^
[ 41%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 42%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 43%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 44%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
[ 45%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 46%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
[ 47%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 48%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 49%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
[ 50%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 51%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 52%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
[ 53%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 54%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 55%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
[ 56%] Linking CXX static library libbamtools.a
[ 56%] Built target BamTools-static
Scanning dependencies of target sniffles
[ 57%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o
[ 58%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp:219:22: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  system(move.c_str());
                      ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_SVs()’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp:293:21: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  system(del.c_str());
                     ^
[ 59%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o
[ 60%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o
[ 61%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o
[ 62%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o
[ 63%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o
[ 64%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o
[ 65%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o
[ 67%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o
[ 68%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o
[ 69%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp: In constructor ‘SWCPUCor::SWCPUCor(int)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp:30:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
  fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement));
                                                                       ^
[ 70%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o
[ 71%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp:154:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
     fprintf(file, "%i", SV->get_length());
                                         ^
[ 72%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:35:89: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr));
                                                                              ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:42:88: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 (file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr));
                                                                              ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:70:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
     fprintf(file, "%i", SV->get_length());
                                         ^
[ 73%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o
[ 74%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o
[ 75%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o
[ 76%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o
[ 77%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs(std::vector<combine_str>&)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp:87:22: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  system(move.c_str());
                      ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs()’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp:159:21: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  system(del.c_str());
                     ^
[ 78%] Linking CXX executable ../../bin/sniffles-core-1.0.5/sniffles
[ 78%] Built target sniffles
Scanning dependencies of target sniffles-debug
[ 79%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/Breakpoint_Tree.cpp.o
[ 80%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Genotyper/Genotyper.cpp.o
[ 81%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Alignment.cpp.o
[ 82%] Building CXX object src/CMakeFiles/sniffles-debug.dir/BamParser.cpp.o
[ 83%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Sniffles.cpp.o
[ 84%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Ignore_Regions.cpp.o
[ 85%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/Intervall_bed.cpp.o
[ 86%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/IntervallList.cpp.o
[ 87%] Building CXX object src/CMakeFiles/sniffles-debug.dir/sub/Detect_Breakpoints.cpp.o
[ 88%] Building CXX object src/CMakeFiles/sniffles-debug.dir/sub/Breakpoint.cpp.o
[ 89%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/IntervallTree.cpp.o
[ 90%] Building CXX object src/CMakeFiles/sniffles-debug.dir/realign/SWCPU.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp: In constructor ‘SWCPUCor::SWCPUCor(int)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp:30:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
  fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement));
                                                                       ^
[ 91%] Building CXX object src/CMakeFiles/sniffles-debug.dir/realign/Realign.cpp.o
[ 92%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/VCFPrinter.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp:154:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
     fprintf(file, "%i", SV->get_length());
                                         ^
[ 93%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/BedpePrinter.cpp.o
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)’:
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:35:89: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr));
                                                                              ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:42:88: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
 (file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr));
                                                                              ^
/home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:70:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
     fprintf(file, "%i", SV->get_length());
                                         ^
[ 94%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/IPrinter.cpp.o
[ 95%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/BinTree.cpp.o
[ 96%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/NGMPrinter.cpp.o
[ 97%] Building CXX object src/CMakeFiles/sniffles-debug.dir/plane-sweep/PlaneSweep_slim.cpp.o
[ 98%] Building CXX object src/CMakeFiles/sniffles-debug.dir/cluster/Cluster_SVs.cpp.o
[100%] Linking CXX executable ../../bin/sniffles-core-1.0.5/sniffles-debug
[100%] Built target sniffles-debug
Installation of Sniffles finished
➜  nextsv git:(master) ✗
BOL

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