Description: Do not override dpkg provided c/cxxflags
Author: Nilesh Patra <nilesh@iki.fi>
Last-Update: 2025-10-30
--- a/Makefile
+++ b/Makefile
@@ -22,8 +22,8 @@
 endif
 #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -DTRACE
 #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC 
-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC 
-export LIBS		= -lz -L $(ZLIB_PATH)
+export CXXFLAGS += -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(CPPFLAGS)
+export LIBS		+= -lz -L $(ZLIB_PATH)
 #export BT_ROOT  = src/utils/BamTools/
 export MKFILE_DIR = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 
--- a/src/filter/Makefile
+++ b/src/filter/Makefile
@@ -1,4 +1,4 @@
 
 all:
-	$(CC) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
+	$(CC) $(CFLAGS) $(CPPFLAGS) -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz $(LDFLAGS)