SpliceJumper installation issues. Particularly with make

Question

[njbernstein]

I'm attempting to install splice jumper (http://www.biomedcentral.com/1471-2105/16/S17/S10, https://github.com/Reedwarbler/SpliceJumper)

So I downloaded the zip, and unzipped it. Then ran make, but there is still no SpliceJumper (I have bamtools installed).

Here is the output from make:

g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c bam_parse.cpp
bam_parse.cpp: In member function 'void BamParse::parseCigar(std::vector<BamTools::CigarOp, std::allocator<BamTools::CigarOp> >&, BamAlignmentRecord*&)':
bam_parse.cpp:57: warning: comparison between signed and unsigned integer expressions
bam_parse.cpp: In member function 'bool BamParse::parseAlignment(int, int, int, int)':
bam_parse.cpp:121: warning: unused variable 'is_set'
bam_parse.cpp: In member function 'void BamParse::getChromNameLength(int, std::string&, int&)':
bam_parse.cpp:275: warning: comparison between signed and unsigned integer expressions
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c Coverage.cpp
Coverage.cpp:454:5: warning: multi-line comment
Coverage.cpp: In member function 'void Coverage::pileupRegion(int, int, int, BamParse&, int*&, Brkpnt*&, int*&, int*&, int*&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::ofstream&, std::string&)':
Coverage.cpp:405: warning: 'clip_pos1' may be used uninitialized in this function
Coverage.cpp:405: warning: 'clip_pos2' may be used uninitialized in this function
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c fai_parser.cpp
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c fasta_parser.cpp
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c ReferenceSeq.cpp
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c algorithms/local_alignment.cpp
algorithms/local_alignment.cpp:29: warning: deprecated conversion from string constant to 'char*'
algorithms/local_alignment.cpp:50: warning: deprecated conversion from string constant to 'char*'
algorithms/local_alignment.cpp:71: warning: deprecated conversion from string constant to 'char*'
algorithms/local_alignment.cpp:81: warning: deprecated conversion from string constant to 'char*'
algorithms/local_alignment.cpp: In member function 'void LocalAlignment::align(int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&, int&)':
algorithms/local_alignment.cpp:1071: warning: comparison between signed and unsigned integer expressions
algorithms/local_alignment.cpp:1071: warning: comparison between signed and unsigned integer expressions
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c CandidateSitesCaller.cpp
CandidateSitesCaller.cpp: In member function 'void CandidateSitesCaller::loadBrkpntInfo(int*&, int*&, int*&, int*&)':
CandidateSitesCaller.cpp:57: warning: unused variable 'clip'
CandidateSitesCaller.cpp: In member function 'void CandidateSitesCaller::callCandidateSites()':
CandidateSitesCaller.cpp:187: warning: unused variable 'idx_start'
CandidateSitesCaller.cpp:137: warning: unused variable 'lclip'
CandidateSitesCaller.cpp:137: warning: unused variable 'rclip'
CandidateSitesCaller.cpp:138: warning: unused variable 'clip'
CandidateSitesCaller.cpp:140: warning: unused variable 'local_cov'
CandidateSitesCaller.cpp: In member function 'void CandidateSitesCaller::outputFeatures(std::string)':
CandidateSitesCaller.cpp:311: warning: comparison between signed and unsigned integer expressions
CandidateSitesCaller.cpp:272: warning: unused variable 'nsplit_map'
CandidateSitesCaller.cpp: In member function 'bool CandidateSitesCaller::searchMapSite(std::string, ReferenceSeq&, std::string, int, int, bool)':
CandidateSitesCaller.cpp:652: warning: comparison between signed and unsigned integer expressions
CandidateSitesCaller.cpp:700: warning: comparison between signed and unsigned integer expressions
CandidateSitesCaller.cpp:753: warning: comparison between signed and unsigned integer expressions
CandidateSitesCaller.cpp: In member function 'void CandidateSitesCaller::getCigarPosLen(std::vector<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int>, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, int> > >&, int, int&, int&, int&, int&)':
CandidateSitesCaller.cpp:824: warning: unused variable 'cnt'
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c TrainingSet.cpp
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c HardClipReads.cpp
HardClipReads.cpp:138: warning: deprecated conversion from string constant to 'char*'
HardClipReads.cpp: In function 'void stk_printstr(const kstring_t*, unsigned int)':
HardClipReads.cpp:157: warning: comparison between signed and unsigned integer expressions
HardClipReads.cpp:159: warning: comparison between signed and unsigned integer expressions
HardClipReads.cpp: In function 'int stk_subseq(const char*, const char*, const char*)':
HardClipReads.cpp:274: warning: comparison between signed and unsigned integer expressions
HardClipReads.cpp:278: warning: comparison between signed and unsigned integer expressions
HardClipReads.cpp:290: warning: comparison between signed and unsigned integer expressions
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -c main.cpp
main.cpp: In function 'int main(int, char**)':
main.cpp:26: warning: unused variable 'refsize'
g++ -O3 -Wall -I../bamtools-master/include -L../bamtools-master/lib -Wl,-rpath,../bamtools-master/lib -o JunctionClassifier_1 public_func.o Alignment.o bam_parse.o Coverage.o fai_parser.o fasta_parser.o ReferenceSeq.o local_alignment.o CandidateSitesCaller.o TrainingSet.o HardClipReads.o main.o \
    -lbamtools -lz -lm

Here is the output from ls:

algorithms     bam_alignment_record.h  bam_parse.o               Coverage.cpp    fai_parser.h      fasta_parser.o     JunctionCaller.cpp    kseq.h             Makefile         public_func.o        ReferenceSeq.h    TrainingSet.cpp
Alignment.cpp  bam_header_record.h     CandidateSitesCaller.cpp  Coverage.h      fai_parser.o      HardClipReads.cpp  JunctionCaller.h      local_alignment.o  Makefile.bak     public_parameters.h  ReferenceSeq.o    TrainingSet.h
Alignment.h    bam_parse.cpp           CandidateSitesCaller.h    Coverage.o      fasta_parser.cpp  HardClipReads.h    JunctionClassifier_1  main.cpp           public_func.cpp  readme.txt           ResultAnalyze     TrainingSet.o
Alignment.o    bam_parse.h             CandidateSitesCaller.o    fai_parser.cpp  fasta_parser.h    HardClipReads.o    khash.h               main.o             public_func.h    ReferenceSeq.cpp

Any Ideas?

[Kristoffer Vitting-Seerup]

Seems the tool have not been updated since it was initially uploaded to github - are you sure you don't want to use a maintained tool?

[Jean-Karim Heriche]

This was posted 3+ years ago, only a few months after the code was made available. I agree it now looks abandoned but that doesn't mean it may not be useful to someone.

[Kristoffer Vitting-Seerup]

hehe! Did not notice that :D

Answer 1

[Jean-Karim Heriche]

I don't see any error, only warnings in the output you provided. Also object files have been generated so it looks like the compilation worked. From the last line of the make output, it looks like the program is named JunctionClassifier_1 which you have in your ls output so I think it all worked fine.

[njbernstein]

Great Thanks!