Author: Michael R. Crusoe <crusoe@debian.org>
Date: Sat Sep 7 15:20:24 2019 +0900
Description: make the vcflib codecopy less bad by using the smithwaterman library
Forwarded: not-needed
--- vg.orig/Makefile
+++ vg/Makefile
@@ -64,11 +64,11 @@
 # necessary on all platforms and suppresses warnings.
 # Also, pkg-config flags need to be made -isystem if our dependency install
 # directory is, or they might put a system HTSlib before ours.
-INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) -I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
+INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) $(shell $(PKG_CONFIG) --cflags libsmithwaterman) -I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
 
 # Define libraries to link vg against.
 LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
-LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack)
+LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph $(shell $(PKG_CONFIG) --libs libfastahack) $(shell $(PKG_CONFIG) --libs libsmithwaterman)
 # We omit Boost Program Options for now; we find it in a platform-dependent way.
 # By default it has no suffix
 BOOST_SUFFIX=""
