edit: I mean version 0.8.1

Hi,

email [email protected] is not working, so I try this way:

I just wanted to compile cnver but ran into problems with both 1.8.1 and
current git.

git clone https://github.com/pashadag/Cnver.git

cd Cnver
./configure
make

[..]
concordancy_analysis.cpp:23:41: warning: ‘typedef’ was ignored in this
declaration [enabled by default]
typedef enum dirEnum { FOR = 0, BACK = 1};
^
concordancy_analysis.cpp: In function ‘int main(int, char*)’:
concordancy_analysis.cpp:203:58: error: ‘getopt’ was not declared in
this scope
while ((ch = getopt(argc, argv, "pcf:b:u:l:t:d:r:m:n:i:")) != -1) {
^
concordancy_analysis.cpp:212:19: error: ‘optarg’ was not declared in
this scope
upperd = atoi(optarg);
^
concordancy_analysis.cpp:238:65: error: ‘optind’ was not declared in
this scope
if (!((upperd >= lowerd) && (lowerd >= 0) && (readLen > 0) && (optind
== argc ) )) {//should be no other parameter
^
make[3]: ** [concordancy_analysis.o] Error 1
make[3]: Leaving directory /scratch/local/install/Cnver/src/cluster' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory/scratch/local/install/Cnver/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/local/install/Cnver'
make: *** [all] Error 2

After adding

include<getopt.h> to concordancy_analysis.cpp I get the next one:

[..]
g++ -g -O2 -o concordancy_analysis concordancy_analysis.o BGZF.o
BamReader.o BamWriter.o -lz
if g++ -DHAVE_CONFIG_H -I. -I. -I../.. -g -O2 -MT
cluster_matepairs.o -MD -MP -MF ".deps/cluster_matepairs.Tpo" -c -o
cluster_matepairs.o cluster_matepairs.cpp;
then mv -f ".deps/cluster_matepairs.Tpo" ".deps/cluster_matepairs.Po";
else rm -f ".deps/cluster_matepairs.Tpo"; exit 1; fi
cluster_matepairs.cpp: In instantiation of ‘bool winScan::load_line()
[with T = std::vectorstd::basic_string]’:
cluster_matepairs.cpp:55:14: required from ‘void
winScan::incr(int&) [with T = std::vectorstd::basic_string]’
cluster_matepairs.cpp:252:20: required from here
cluster_matepairs.cpp:67:34: error: ‘make_T’ was not declared in this
scope, and no declarations were found by argument-dependent lookup at
the point of instantiation [-fpermissive]
buf.push_back(make_T(s, dummyT));
^
cluster_matepairs.cpp:84:16: note: ‘std::vectorstd::basic_string<char

make_T(std::string&, std::vectorstd::basic_string&)’ declared
here, later in the translation unit
vector make_T (string & s, vector & dummy) {
^
make[3]: *** [cluster_matepairs.o] Fehler 1
make[3]: Verlasse Verzeichnis '/tmp/cnver/Cnver/src/cluster'
make[2]: *** [all-recursive] Fehler 1
make[2]: Verlasse Verzeichnis '/tmp/cnver/Cnver/src'
make[1]: *** [all-recursive] Fehler 1
make[1]: Verlasse Verzeichnis '/tmp/cnver/Cnver'
make: *** [all] Fehler 2

This is Ubuntu 14.04 (64bit), g++ (Ubuntu 4.8.2-19ubuntu1) 4.8.2

Same results at work, homemade linux 64bit, g++ (GCC) 4.8.2

As I am not really familiar with C/C++ I assume that there are some
requisites missing?

Can you help?

Thanks,
Sven