From 294a31624c671e0f5e3cc112bbfcec1d766c40e6 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 27 Mar 2019 09:23:37 +0100
Subject: [PATCH] version 1.0.32: compilation with libsuma

---
 Makefile  | 25 ++++++++++---------------
 global.mk | 25 +++++--------------------
 sumalibs  |  2 +-
 sumatra.c |  2 +-
 4 files changed, 17 insertions(+), 37 deletions(-)

diff --git a/Makefile b/Makefile
index 8736691..329af02 100644
--- a/Makefile
+++ b/Makefile
@@ -1,14 +1,13 @@
-EXEC=sumatra
+EXEC = sumatra
 
-SUMATRA_SRC= sumatra.c \
-			 mtcompare_sumatra.c
+SUMATRA_SRC = sumatra.c \
+			  mtcompare_sumatra.c
 			              
-SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATRA_SRC))
+SUMATRA_OBJ = $(patsubst %.c,%.o,$(SUMATRA_SRC))
 
+SRCS = $(SUMATRA_SRC)
 
-SRCS= $(SUMATRA_SRC)
-
-LIB= -lfasta -llcs -lfile -lutils -lz -lm
+LIB = -lsuma -lz -lm
 
 include ./global.mk
 
@@ -23,8 +22,8 @@ all: $(EXEC)
 
 # executable compilation and link
 
-sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
-	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH) $(LIB)
+sumatra: $(SUMATRA_OBJ) $(LIBSUMA)
+	$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBSUMAPATH) $(LIB)
 	
 ########
 #
@@ -33,12 +32,8 @@ sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
-	rm -f *.P
+	rm -f $(SUMATRA_OBJ)	
 	rm -f $(EXEC)
-	$(MAKE) -C ./sumalibs/libfasta clean
-	$(MAKE) -C ./sumalibs/liblcs clean
-	$(MAKE) -C ./sumalibs/libfile clean
-	$(MAKE) -C ./sumalibs/libutils clean
+	$(MAKE) -C ./sumalibs clean
 
 		
diff --git a/global.mk b/global.mk
index 9b7651f..f03405d 100644
--- a/global.mk
+++ b/global.mk
@@ -1,20 +1,14 @@
 
-LIBFASTAPATH = -L./sumalibs/libfasta
-LIBLCSPATH   = -L./sumalibs/liblcs
-LIBFILEPATH  = -L./sumalibs/libfile
-LIBUTILSPATH = -L./sumalibs/libutils
+LIBSUMAPATH = -L./sumalibs
 
-LIBFASTA = ./sumalibs/libfasta/libfasta.a
-LIBLCS   = ./sumalibs/liblcs/liblcs.a
-LIBFILE  = ./sumalibs/libfile/libfile.a
-LIBUTILS = ./sumalibs/libutils/libutils.a
+LIBSUMA = ./sumalibs/libsuma.a
 
 CC=gcc
 LDFLAGS=
 
 
 ifeq ($(CC),gcc)
-        CFLAGS = -O3 -s -DOMP_SUPPORT -fopenmp -w
+        CFLAGS = -O3 -s -DOMP_SUPPORT -w
 else
         CFLAGS = -O3 -w
 endif
@@ -32,14 +26,5 @@ default: all
 #
 ########
 
-./sumalibs/libfasta/libfasta.a:
-	$(MAKE) -C ./sumalibs/libfasta
-
-./sumalibs/liblcs/liblcs.a:
-	$(MAKE) -C ./sumalibs/liblcs
-
-./sumalibs/libfile/libfile.a:
-	$(MAKE) -C ./sumalibs/libfile
-
-./sumalibs/libutils/libutils.a:
-	$(MAKE) -C ./sumalibs/libutils
\ No newline at end of file
+./sumalibs/libsuma.a:
+	$(MAKE) -C ./sumalibs
diff --git a/sumalibs b/sumalibs
index 0491294..ed56cb1 160000
--- a/sumalibs
+++ b/sumalibs
@@ -1 +1 @@
-Subproject commit 049129488ed96b03a5976512fe328dadeb72ace9
+Subproject commit ed56cb1d6b1e60a297cd0d1c67a4e17e4c59d202
diff --git a/sumatra.c b/sumatra.c
index 7e62ca2..d3a3345 100644
--- a/sumatra.c
+++ b/sumatra.c
@@ -20,7 +20,7 @@
 #include "./sumalibs/libutils/utilities.h"
 #include "mtcompare_sumatra.h"
 
-#define VERSION "1.0.31"
+#define VERSION "1.0.32"
 
 
 /* ----------------------------------------------- */