From ed56cb1d6b1e60a297cd0d1c67a4e17e4c59d202 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 27 Mar 2019 09:00:48 +0100
Subject: [PATCH] Now compiling in one single library

---
 Makefile           |  46 +++++++++++++++++++++++++++++++++++++++++++++
 global.mk          |  10 ----------
 libfasta/.DS_Store | Bin 6148 -> 0 bytes
 libfasta/Makefile  |  33 --------------------------------
 libfile/.DS_Store  | Bin 6148 -> 0 bytes
 libfile/Makefile   |  25 ------------------------
 liblcs/.DS_Store   | Bin 6148 -> 0 bytes
 liblcs/Makefile    |  25 ------------------------
 libsse/.DS_Store   | Bin 6148 -> 0 bytes
 libutils/.DS_Store | Bin 6148 -> 0 bytes
 libutils/Makefile  |  25 ------------------------
 11 files changed, 46 insertions(+), 118 deletions(-)
 create mode 100755 Makefile
 delete mode 100755 global.mk
 delete mode 100644 libfasta/.DS_Store
 delete mode 100755 libfasta/Makefile
 delete mode 100644 libfile/.DS_Store
 delete mode 100755 libfile/Makefile
 delete mode 100644 liblcs/.DS_Store
 delete mode 100755 liblcs/Makefile
 delete mode 100644 libsse/.DS_Store
 delete mode 100644 libutils/.DS_Store
 delete mode 100755 libutils/Makefile

diff --git a/Makefile b/Makefile
new file mode 100755
index 0000000..7921df4
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,46 @@
+
+SOURCES = libfasta/fasta_header_parser.c \
+		  libfasta/fasta_seq_writer.c \
+		  libfasta/fasta_header_handler.c \
+		  libfasta/header_mem_handler.c \
+          libfasta/sequence.c \
+          libfile/fileHandling.c \
+          liblcs/sse_banded_LCS_alignment.c \
+		  liblcs/upperband.c \
+		  libutils/utilities.c \
+          libutils/debug.c  
+                   
+SRCS=$(SOURCES)
+         
+OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
+
+LIBFILE = libsuma.a
+
+RANLIB = ranlib
+
+CC=gcc
+
+LDFLAGS=
+
+CFLAGS = -O3 -w
+
+default: all
+
+all: $(LIBFILE)
+
+%.o: %.c
+	$(CC) $(CFLAGS) -c -o $@ $< $(LIB)
+
+libfasta/fasta_header_parser.c: libfasta/fasta_header_parser.l
+	flex -Pheader_yy -t $< > $@
+
+libfasta/dic_parser.c: libfasta/dic_parser.l
+	lex -Phashtable_yy -t $< > $@
+
+clean:
+	rm -rf $(OBJECTS) $(LIBFILE)
+
+$(LIBFILE): $(OBJECTS)
+	ar -cr $@ $?
+	$(RANLIB) $@
+
diff --git a/global.mk b/global.mk
deleted file mode 100755
index c58123e..0000000
--- a/global.mk
+++ /dev/null
@@ -1,10 +0,0 @@
-
-CC=gcc
-LDFLAGS=
-
-CFLAGS = -O3 -w
-
-default: all
-
-%.o: %.c
-	$(CC) $(CFLAGS) -c -o $@ $< $(LIB)
diff --git a/libfasta/.DS_Store b/libfasta/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/libfasta/Makefile b/libfasta/Makefile
deleted file mode 100755
index 97cf5ec..0000000
--- a/libfasta/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-
-SOURCES = fasta_header_parser.c \
-		  fasta_seq_writer.c \
-		  fasta_header_handler.c \
-		  header_mem_handler.c \
-          sequence.c 
-                   
-SRCS=$(SOURCES)
-
-         
-OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
-
-LIBFILE = libfasta.a
-RANLIB = ranlib
-
-
-include ../global.mk
-
-all: $(LIBFILE)
-
-fasta_header_parser.c: fasta_header_parser.l
-	flex -Pheader_yy -t $< > $@
-
-dic_parser.c: dic_parser.l
-	lex -Phashtable_yy -t $< > $@
-
-clean:
-	rm -rf $(OBJECTS) $(LIBFILE)
-	rm -f *.a
-
-$(LIBFILE): $(OBJECTS)
-	ar -cr $@ $?
-	$(RANLIB) $@
diff --git a/libfile/.DS_Store b/libfile/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/libfile/Makefile b/libfile/Makefile
deleted file mode 100755
index fc12708..0000000
--- a/libfile/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-
-SOURCES = fileHandling.c
-
-         
-SRCS=$(SOURCES)
-
-         
-OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
-
-LIBFILE= libfile.a
-RANLIB=ranlib
-
-
-include ../global.mk
-
-all: $(LIBFILE)
-
-clean:
-	rm -rf $(OBJECTS) $(LIBFILE)
-	rm -f *.P
-	rm -f *.a
-
-$(LIBFILE): $(OBJECTS)
-	ar -cr $@ $?
-	$(RANLIB) $@
diff --git a/liblcs/.DS_Store b/liblcs/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/liblcs/Makefile b/liblcs/Makefile
deleted file mode 100755
index 43a787c..0000000
--- a/liblcs/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-
-SOURCES = sse_banded_LCS_alignment.c  \
-		  upperband.c
-         
-SRCS=$(SOURCES)
-
-         
-OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
-
-LIBFILE= liblcs.a
-RANLIB=ranlib
-
-
-include ../global.mk
-
-all: $(LIBFILE)
-
-clean:
-	rm -rf $(OBJECTS) $(LIBFILE)
-	rm -f *.P
-	rm -f *.a
-
-$(LIBFILE): $(OBJECTS)
-	ar -cr $@ $?
-	$(RANLIB) $@
diff --git a/libsse/.DS_Store b/libsse/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/libutils/.DS_Store b/libutils/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/libutils/Makefile b/libutils/Makefile
deleted file mode 100755
index 8428d77..0000000
--- a/libutils/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-
-SOURCES = utilities.c  \
-          debug.c      
-         
-SRCS=$(SOURCES)
-
-         
-OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
-
-LIBFILE= libutils.a
-RANLIB=ranlib
-
-
-include ../global.mk
-
-all: $(LIBFILE)
-
-clean:
-	rm -rf $(OBJECTS) $(LIBFILE)
-	rm -f *.P
-	rm -f *.a
-
-$(LIBFILE): $(OBJECTS)
-	ar -cr $@ $?
-	$(RANLIB) $@