Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: make the vcflib codecopy less bad by using the smithwaterman library
--- vg.orig/Makefile
+++ vg/Makefile
@@ -31,12 +31,12 @@
 CXXFLAGS := -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP $(CXXFLAGS)
 
 # Set include flags. All -I options need to go in here, so the first directory listed is genuinely searched first.
-INCLUDE_FLAGS:=$(shell pkg-config --cflags libfastahack) -I$(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic -I$(CWD)/$(INC_DIR)/sonLib $(shell pkg-config --cflags cairo jansson)
+INCLUDE_FLAGS:=$(shell pkg-config --cflags libfastahack) -I$(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic -I$(CWD)/$(INC_DIR)/sonLib $(shell pkg-config --cflags cairo jansson) $(shell pkg-config --cflags libsmithwaterman)
 
 # Define libraries to link against. Make sure to always link statically against
 # htslib and libdeflate and Protobuf so that we can use position-dependent code
 # there for speed.
-LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack)
+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph $(shell pkg-config --libs libfastahack) $(shell pkg-config --libs libsmithwaterman)
 # Use pkg-config to find Cairo and all the libs it uses
 LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson)
 
