[Seqan-dev] Error with samtools library

["Schulze, Jakob" <SchulzeJa@rki.de>]

Hi everyone,
I came across some code which uses the samtools library. Together with seqan there is an error which seems to come from samtools but I do not know why. Since I am not the author of the samtools include I cannot say much about the corresponding lines in the CMakeLists.txt
But since commenting out seqan from the main.cpp solves the error, I imagined this has something to do with seqan.

I provided a minimal example with a main.cpp and a CMakeLists, which hopefully (on my pc it does) reproduces the error. Please note, that I did use absolute paths for CMAKE_MODULE_PATH and SEQAN_INCLUDE_PATH. You would need to change these accordingly.

Best Regards,
Jakob

PS: Any progress on my last question concerning BamTagsDict?

PPS: terminal output with error message (inside build directory)
==================================================================================================================
$ cmake ..
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- 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
-- Looking for include file execinfo.h
-- Looking for include file execinfo.h - found
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
--   Determined version is 2.0.2
bam_reheader.c: In function ‘bam_reheader’:
bam_reheader.c:36:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
kprobaln.c: In function ‘kpa_glocal’:
kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
misc/md5.c: In function ‘MD5Final’:
misc/md5.c:151:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((uint32_t *) ctx->in)[14] = ctx->bits[0];
     ^
misc/md5.c:152:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((uint32_t *) ctx->in)[15] = ctx->bits[1];
     ^
misc/md5.c: In function ‘MD5Final’:
misc/md5.c:151:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((uint32_t *) ctx->in)[14] = ctx->bits[0];
     ^
misc/md5.c:152:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((uint32_t *) ctx->in)[15] = ctx->bits[1];
     ^
-- Configuring done
-- Generating done
-- Build files have been written to: /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build




$ make
Scanning dependencies of target main
[100%] Building CXX object CMakeFiles/main.dir/main.cpp.o
In file included from /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2/bam.h:48:0,
                 from /home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2/sam.h:29,
                 from /home/schulzeja/masterthesis/workDir/seqanTestForReport2/main.cpp:1:
/home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2/htslib-1.2.1/htslib/bgzf.h:38:29: error: expected unqualified-id before numeric constant
 #define BGZF_MAX_BLOCK_SIZE 0x10000
                             ^
/home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/iostream_bgzf.h:25:16: note: in expansion of macro ‘BGZF_MAX_BLOCK_SIZE’
 const unsigned BGZF_MAX_BLOCK_SIZE = 64 * 1024;
                ^
/home/schulzeja/masterthesis/workDir/seqanTestForReport2/build/samtools-1.2/htslib-1.2.1/htslib/bgzf.h:37:29: error: expected unqualified-id before numeric constant
 #define BGZF_BLOCK_SIZE     0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
                             ^
/home/schulzeja/masterthesis/tools/seqan-src/include/seqan/stream/iostream_bgzf.h:32:16: note: in expansion of macro ‘BGZF_BLOCK_SIZE’
 const unsigned BGZF_BLOCK_SIZE = BGZF_MAX_BLOCK_SIZE - BGZF_BLOCK_HEADER_LENGTH - BGZF_BLOCK_FOOTER_LENGTH - ZLIB_BLOCK_OVERHEAD;
                ^
/home/schulzeja/masterthesis/workDir/seqanTestForReport2/main.cpp:5:14: warning: unused parameter ‘argc’ [-Wunused-parameter]
 int main(int argc, char* argv[]) {
              ^
/home/schulzeja/masterthesis/workDir/seqanTestForReport2/main.cpp:5:31: warning: unused parameter ‘argv’ [-Wunused-parameter]
 int main(int argc, char* argv[]) {
                               ^
CMakeFiles/main.dir/build.make:54: recipe for target 'CMakeFiles/main.dir/main.cpp.o' failed
make[2]: *** [CMakeFiles/main.dir/main.cpp.o] Error 1
CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/main.dir/all' failed
make[1]: *** [CMakeFiles/main.dir/all] Error 2
Makefile:75: recipe for target 'all' failed
make: *** [all] Error 2
====================================================================================================================

#include "sam.h"
#include <seqan/bam_io.h>
using namespace seqan;

int main(int argc, char* argv[]) {
  return 1;
}

##############
### Header ###

cmake_minimum_required (VERSION 2.8)
project (Main)

# Set the version number 
set (Main_VERSION_MAJOR 0)
set (Main_VERSION_MINOR 2)

# Set flags for compilation
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -g -pthread -W -Wall -std=gnu++11 -O2")

# add the binary tree to the search path for include files
include_directories("${PROJECT_BINARY_DIR}")



#############################
### setup seqan libraries ###

set (CMAKE_MODULE_PATH "/home/schulzeja/masterthesis/tools/seqan-src/util/cmake")
set (SEQAN_INCLUDE_PATH "/home/schulzeja/masterthesis/tools/seqan-src/include/")

# Configure SeqAn, enabling features for libbz2 and zlib.
set (SEQAN_FIND_DEPENDENCIES ZLIB BZip2)
find_package (SeqAn REQUIRED)

# Add include directories, defines, and flags for SeqAn (and its dependencies).
include_directories (${SEQAN_INCLUDE_DIRS})
add_definitions (${SEQAN_DEFINITIONS})
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")



#############################################
### download & build the Samtools library ###

file(DOWNLOAD "http://downloads.sourceforge.net/project/samtools/samtools/1.2/samtools-1.2.tar.bz2"; ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2.tar.bz2)
execute_process(COMMAND tar xf ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2.tar.bz2 )
execute_process(COMMAND make -s -C samtools-1.2 )
INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2 )
INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2/htslib-1.2.1 )
LINK_DIRECTORIES( ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2 ${CMAKE_CURRENT_BINARY_DIR}/samtools-1.2/htslib-1.2.1 )



#############################
### Build the executables ###

add_executable (main main.cpp)
target_link_libraries (main ${SEQAN_LIBRARIES} hts)