can't install about repeatseq HOT 7 OPEN

I know it's been a hot minute, but here is how I built this:

$ git clone https://github.com/adaptivegenome/repeatseq
$ cd repeatseq
$ git clone https://github.com/pezmaster31/bamtools
$ git clone https://github.com/ekg/fastahack
$ cd bamtools
$ git checkout split-fix
$ mkdir build
$ cd build
$ cmake ../
$ make
$ cd ../fastahack
$ make
$ cd ..
$ make
$ export LD_LIBRARY_PATH=/path/to/bamtools/lib:$LD_LIBRARY_PATH
$ ./repeatseq

Not enough arguments given. Exiting..

-----------------------------------------------------------

RepeatSeq v0.8.2

Usage:   repeatseq [options] <in.bam> <in.fasta> <in.regions>

Options: -r             use only a specific read length or range of read lengths (e.g. LENGTH or MIN:MAX)
         -L             required number of reference matching bases BEFORE the repeat [3]
         -R             required number of reference matching bases AFTER the repeat [3]
         -M             minimum mapping quality for a read to be used for allele determination
         -multi         exclude reads flagged with the XT:A:R tag
         -pp            exclude reads that are not properly paired (for PE reads only)
         -emitconfidentsites            report all confident genotypes even if they do not vary from ref

         -haploid       assume a haploid rather than diploid genome

         -repeatseq     write .repeatseq file containing additional information about reads
         -calls         write .calls file
         -t             include user-defined tag in the output filename
         -o             number of flanking bases to output from each read

-----------------------------------------------------------

Hope this helps.

from repeatseq.

Hi, did you solve this? I also got this error when installing repeatseq.

from repeatseq.

I couldn't install either.
I got the following error
g++ -c -O3 -Ibamtools/src repeatseq.cpp
In file included from fastahack/Fasta.h:19:0,
from repeatseq.h:22,
from repeatseq.cpp:27:
fastahack/LargeFileSupport.h:14:0: warning: "fseek64" redefined
#define fseek64(a,b,c) fseeko(a,b,c)

In file included from bamtools/src/api/api_global.h:13:0,
from bamtools/src/api/BamAux.h:19,
from bamtools/src/api/BamAlignment.h:18,
from bamtools/src/api/BamReader.h:14,
from repeatseq.h:18,
from repeatseq.cpp:27:
bamtools/src/shared/bamtools_global.h:46:0: note: this is the location of the previous definition
#define fseek64(a, b, c) fseeko(a, b, c)

repeatseq.cpp: In function ‘bool fileCheck(std::__cxx11::string)’:
repeatseq.cpp:1398:9: error: cannot convert ‘std::ifstream {aka std::basic_ifstream}’ to ‘bool’ in return
return ifile;
^~~~~
makefile:13: recipe for target 'repeatseq.o' failed
make: *** [repeatseq.o] Error 1

Any suggetions?

from repeatseq.

I know it's been a hot minute, but here is how I built this:

$ git clone https://github.com/adaptivegenome/repeatseq
$ cd repeatseq
$ git clone https://github.com/pezmaster31/bamtools
$ git clone https://github.com/ekg/fastahack
$ cd bamtools
$ git checkout split-fix
$ mkdir build
$ cd build
$ cmake ../
$ make
$ cd ../fastahack
$ make
$ cd ..
$ make
$ export LD_LIBRARY_PATH=/path/to/bamtools/lib:$LD_LIBRARY_PATH
$ ./repeatseq

Not enough arguments given. Exiting..

-----------------------------------------------------------

RepeatSeq v0.8.2

Usage:   repeatseq [options] <in.bam> <in.fasta> <in.regions>

Options: -r             use only a specific read length or range of read lengths (e.g. LENGTH or MIN:MAX)
         -L             required number of reference matching bases BEFORE the repeat [3]
         -R             required number of reference matching bases AFTER the repeat [3]
         -M             minimum mapping quality for a read to be used for allele determination
         -multi         exclude reads flagged with the XT:A:R tag
         -pp            exclude reads that are not properly paired (for PE reads only)
         -emitconfidentsites            report all confident genotypes even if they do not vary from ref

         -haploid       assume a haploid rather than diploid genome

         -repeatseq     write .repeatseq file containing additional information about reads
         -calls         write .calls file
         -t             include user-defined tag in the output filename
         -o             number of flanking bases to output from each read

-----------------------------------------------------------

Hope this helps.

I use your method to install Repeatseq,but when make, there was also error as follow:
repeatseq.cpp: In function 'bool fileCheck(std::__cxx11::string)':
repeatseq.cpp:1398:9: error: cannot convert 'std::ifstream {aka std::basic_ifstream}' to 'bool' in return
return ifile;
^~~~~
makefile:13: recipe for target 'repeatseq.o' failed
make: *** [repeatseq.o] Error 1

I would be appreciated if there is any suggestions.

from repeatseq.

I use your method to install Repeatseq,but when make, there was also error as follow:
repeatseq.cpp: In function 'bool fileCheck(std::__cxx11::string)':
repeatseq.cpp:1398:9: error: cannot convert 'std::ifstream {aka std::basic_ifstream}' to 'bool' in return
return ifile;
^~~~~
makefile:13: recipe for target 'repeatseq.o' failed
make: *** [repeatseq.o] Error 1

I would be appreciated if there is any suggestions.

What gcc version are you using? I'd suggest trying a more recent version 8 or 9.

from repeatseq.

I use your method to install Repeatseq,but when make, there was also error as follow:
repeatseq.cpp: In function 'bool fileCheck(std::__cxx11::string)':
repeatseq.cpp:1398:9: error: cannot convert 'std::ifstream {aka std::basic_ifstream}' to 'bool' in return
return ifile;
^~~~~
makefile:13: recipe for target 'repeatseq.o' failed
make: *** [repeatseq.o] Error 1
I would be appreciated if there is any suggestions.

What gcc version are you using? I'd suggest trying a more recent version 8 or 9.

Today, I already installed gcc9.1.0 version , but when making,there was the same problem as like above. So, please give me some advice.

from repeatseq.

Hi,
I have fixed the error changing line 1398 (funcbool fileCheck(string strFilename)) from
return ifile;
to
return ifile.good();

Good luck

from repeatseq.