--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMSAME/src/Makefile	Sat Dec 15 18:04:10 2018 -0500
@@ -0,0 +1,23 @@
+CC=gcc
+CXX=g++
+CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall #-DVERBOSE
+BIN=../bin
+
+all: IMSAME revcomp combine covident
+
+
+
+IMSAME: IMSAME.c
+	$(CC) $(CFLAGS) alignmentFunctions.c -lpthread -lm commonFunctions.c -msse -lm IMSAME.c -lpthread -lm -o $(BIN)/IMSAME
+	
+revcomp: reverseComplement.c
+	$(CC) $(CFLAGS) commonFunctions.c -lm  reverseComplement.c -o $(BIN)/revComp
+	
+combine: combine_reads.c
+	$(CC) $(CFLAGS) commonFunctions.c -lm combine_reads.c -o $(BIN)/combine
+
+covident: covident.c
+	$(CC) $(CFLAGS) covident.c -o $(BIN)/combine
+
+clean:
+	rm -rf $(BIN)/IMSAME $(BIN)/revComp $(BIN)/combine