update zlib options

Author: Yenaled

CMakeLists.txt

@@ -49,18 +49,21 @@ endif(BUILD_FUNCTESTING)
 
 include(ExternalProject)
 
+
+
 if (ZLIBNG)
     message("zlib-ng enabled.")
     ExternalProject_Add(zlib-ng
     PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
     SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
     BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=${PREFIX}
-    BUILD_COMMAND cd build && make
+    CONFIGURE_COMMAND mkdir -p zlib-ng && cd zlib-ng && cmake .. -DZLIB_COMPAT=ON -DZLIB_ENABLE_TESTS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX}
+    BUILD_COMMAND cd zlib-ng && make
     INSTALL_COMMAND ""
     )
 endif(ZLIBNG)
 
+
 if (USE_HTSLIB)
     message("using htslib")
     ExternalProject_Add(htslib

src/CMakeLists.txt

@@ -36,12 +36,12 @@ endif(NOT ZLIBNG)
 
 if (ZLIBNG)
     add_definitions(-DSPLITCODE_USE_ZLIB_NG)
-    include_directories(../ext/zlib-ng/build)
+    include_directories(../ext/zlib-ng/zlib-ng)
     include_directories(../ext/zlib-ng)
     if(WIN32)
-    target_link_libraries(splitcode ${CMAKE_CURRENT_SOURCE_DIR}/../ext/zlib-ng/build/libz-ng.lib)
+    target_link_libraries(splitcode ${CMAKE_CURRENT_SOURCE_DIR}/../ext/zlib-ng/zlib-ng/libz.lib)
     else()
-    target_link_libraries(splitcode ${CMAKE_CURRENT_SOURCE_DIR}/../ext/zlib-ng/build/libz-ng.a)
+    target_link_libraries(splitcode ${CMAKE_CURRENT_SOURCE_DIR}/../ext/zlib-ng/zlib-ng/libz.a)
     endif(WIN32)
 endif(ZLIBNG)
 

src/ProcessReads.h

@@ -16,30 +16,24 @@
 #include <atomic>
 #include <condition_variable>
 
-#include "common.h"
 
 #ifdef SPLITCODE_USE_ZLIB_NG
 #ifndef WITH_GZFILEOP
 #define WITH_GZFILEOP
 #endif
-#include "zlib-ng.h"
-constexpr auto gzopen = zng_gzopen;
-constexpr auto gzclose = zng_gzclose;
-constexpr auto gzwrite = zng_gzwrite;
-constexpr auto gzdopen = zng_gzdopen;
+#include "zlib-ng/zlib.h"
 #else
 #include <zlib.h>
 #endif
 
+
+#include "common.h"
+
 #ifndef KSEQ_INIT_READY
 #define KSEQ_INIT_READY
-#ifndef SPLITCODE_USE_ZLIB_NG
 KSEQ_INIT(gzFile, gzread)
-#else
-KSEQ_INIT(gzFile, zng_gzread)
-#endif
 #endif
-  
+ 
 class MasterProcessor;
 
 int64_t ProcessReads(MasterProcessor& MP, const  ProgramOptions& opt);