Actualiser .gitmodules

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "sumalibs"]
 	path = sumalibs
-	url = https://git.metabarcoding.org/obitools/sumalibs.git
+	url = https://forge.metabarcoding.org/obitools/sumalibs.git

Makefile

@@ -1,16 +1,17 @@
-EXEC=sumaclust
+PREFIX=/usr/local
 
-SUMACLUST_SRC= sumaclust.c \
-               mtcompare_sumaclust.c
+CFLAGS=-I$(PREFIX)/include
 
+EXEC = sumaclust
 
-SUMACLUST_OBJ= $(patsubst %.c,%.o,$(SUMACLUST_SRC))
+SUMACLUST_SRC = sumaclust.c \
+                mtcompare_sumaclust.c
 
+SUMACLUST_OBJ = $(patsubst %.c,%.o,$(SUMACLUST_SRC))
 
-SRCS= $(SUMACLUST_SRC)
-
-LIB= -lfasta -llcs -lfile -lutils -lm #-ll
+SRCS = $(SUMACLUST_SRC)
 
+LIB = -lsuma -lm #-ll
 
 include ./global.mk
 
@@ -31,8 +32,8 @@ else
         LFLAGS = 
 endif
 
-sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
-	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH)
+sumaclust: $(SUMACLUST_OBJ) $(LIBSUMA)
+	$(CC) $(LDFLAGS) -o $@ $(LFLAGS) $(SUMACLUST_OBJ) $(LIB) $(LIBSUMAPATH)
 	
 ########
 #
@@ -41,12 +42,11 @@ sumaclust: $(SUMACLUST_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
 ########
 
 clean:
-	rm -f *.o	
-	rm -f *.P
+	rm -f $(SUMACLUST_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
 
+install: all
+	install -d $(DESTDIR)$(PREFIX)/bin/
+	install -m 755 $(EXEC) $(DESTDIR)$(PREFIX)/bin/
 

global.mk

@@ -1,13 +1,7 @@
 
-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=
@@ -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
+./sumalibs/libsuma.a:
+	$(MAKE) -C ./sumalibs

mtcompare_sumaclust.c

@@ -15,10 +15,10 @@
 #include <math.h>
 #include <sys/time.h>
 
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/libutils/utilities.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "sumalibs/libfasta/sequence.h"
+#include "sumalibs/libutils/utilities.h"
+#include "sumalibs/liblcs/upperband.h"
+#include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
 
 #include "sumaclust.h"
 

sumaclust.c

@@ -12,18 +12,18 @@
 #include <math.h>
 #include <sys/time.h>
 
-#include "./sumalibs/libutils/utilities.h"
-#include "./sumalibs/libfasta/sequence.h"
-#include "./sumalibs/libfasta/fasta_header_parser.h"
-#include "./sumalibs/libfasta/fasta_header_handler.h"
-#include "./sumalibs/libfasta/fasta_seq_writer.h"
-#include "./sumalibs/liblcs/upperband.h"
-#include "./sumalibs/liblcs/sse_banded_LCS_alignment.h"
+#include "sumalibs/libutils/utilities.h"
+#include "sumalibs/libfasta/sequence.h"
+#include "sumalibs/libfasta/fasta_header_parser.h"
+#include "sumalibs/libfasta/fasta_header_handler.h"
+#include "sumalibs/libfasta/fasta_seq_writer.h"
+#include "sumalibs/liblcs/upperband.h"
+#include "sumalibs/liblcs/sse_banded_LCS_alignment.h"
 
 #include "mtcompare_sumaclust.h"
 #include "sumaclust.h"
 
-#define VERSION "1.0.20"
+#define VERSION "1.0.36"
 
 
 /* ----------------------------------------------- */
@@ -585,7 +585,7 @@ void putSeqInCluster(fastaSeqPtr* seq, fastaSeqPtr* center, double score)
 }
 
 
-int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
+int compare(fastaSeqPtr* db, int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
 		double max_ratio)
 {
 	double       score;
@@ -723,7 +723,7 @@ int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL nor
 	free(iseq1-sizeForSeqs+lmax);
 	free(iseq2-sizeForSeqs+lmax);
 
-	if (normalize && reference == ALILEN)
+	if (normalize && (reference == ALILEN))
 		free(address);
 
 	return(k);
@@ -1037,7 +1037,6 @@ int main(int argc, char** argv)
 	// FASTA file
 	if (printFASTA)
 	{
-
 		if (printFASTAtofile)
 		{
 			FASTA_output = fopen(FASTA_file_name, "w");

sumaclust_user_manual.md

@@ -29,7 +29,8 @@ Untar the archive, go into the newly created directory and compile:
 ```
 tar –zxvf sumaclust_v[x.x.xx].tar.gz
 cd sumaclust_v[x.x.xx]
-make
+make -C sumalibs install
+make install
 ```
 
 You can compile Sumaclust with `clang`, which deactivates `OpenMP`, with: