Actualiser libsse/_sse.h

bug

Makefile

@@ -0,0 +1,56 @@
+PREFIX=/usr/local
+
+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) $@
+
+install: all
+	install -d $(DESTDIR)$(PREFIX)/lib/
+	install -m 644 $(LIBFILE) $(DESTDIR)$(PREFIX)/lib/
+	install -d $(DESTDIR)$(PREFIX)/include/
+	for lib in libfasta liblcs libsse libutils libfile ; do \
+		install -d $(DESTDIR)$(PREFIX)/include/$$lib ; \
+		cp $$lib/*.h $(DESTDIR)$(PREFIX)/include/$$lib ; \
+	done
+

global.mk

@@ -1,10 +0,0 @@
-
-CC=gcc
-LDFLAGS=
-
-CFLAGS = -O3 -w
-
-default: all
-
-%.o: %.c
-	$(CC) $(CFLAGS) -c -o $@ $< $(LIB)

libfasta/Makefile

@@ -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) $@

libfasta/fasta_header_handler.c

@@ -69,34 +69,15 @@ char* fastaSeqPtr_header_add_field(fastaSeqPtr seq, char* name, char* value)
 element_from_header* table_header_add_field(element_from_header* header, char* name, char* value)
 {
 	int nbf;
-	int i, j;
-	element_from_header* new_header;
-
 	nbf = atoi(header[0].value);
-	new_header = (element_from_header*) realloc(header, ((nbf+1)*sizeof(element_from_header)));
+	nbf++;
-
+	header = (element_from_header*) realloc(header, (nbf+1)*sizeof(element_from_header));
-	i=0;
+	header[nbf].name = (char*) malloc((1+strlen(name))*sizeof(char));
-	while ((strcmp(new_header[i].name, "definition") != 0) && (i < nbf))
+	strcpy(header[nbf].name, name);
-		i++;
+	header[nbf].value = (char*) malloc((1+strlen(value))*sizeof(char));
-
+	strcpy(header[nbf].value, value);
-	if (strcmp(new_header[i].name, "definition") == 0)
+	sprintf(header[0].value, "%d", nbf);
-	{
+	return(header);
-		j = nbf-1;
-		while (strcmp(new_header[j].name, "definition") == 0)
-		{
-			new_header[j+1].name = new_header[j].name;
-			new_header[j+1].value = new_header[j].value;
-			j--;
-		}
-	}
-
-	new_header[i].name = (char*) malloc((1+strlen(name))*sizeof(char));
-	strcpy(new_header[i].name, name);
-	new_header[i].value = (char*) malloc((1+strlen(value))*sizeof(char));
-	strcpy(new_header[i].value, value);
-	sprintf(new_header[0].value, "%d", nbf+1);
-
-	return(new_header);
 }
 
 
@@ -105,7 +86,7 @@ void free_header_table(element_from_header* header)
 	int i;
 	int nbf = atoi(header[0].value);
 
-	for (i = 0; i < nbf; i++)
+	for (i = 0; i <= nbf; i++)
 	{
 		free((header[i]).name);
 	    free((header[i]).value);
@@ -120,7 +101,7 @@ char* getItemFromHeader(char* name, element_from_header* header)
 	int nbf;
 	int i;
 	nbf = atoi(header[0].value);
-	for (i = 1; i < nbf; i++)
+	for (i = 1; i <= nbf; i++)
 	{
 		if (strcmp(header[i].name,name)==0)
 			value = header[i].value;
@@ -134,7 +115,7 @@ void changeValue(element_from_header* header, char* name, char* newValue)
 	int i;
 	int nbf = atoi(header[0].value);
 
-	for (i = 1; i < nbf; i++)
+	for (i = 1; i <= nbf; i++)
 	{
 		if (strcmp(header[i].name, name)==0)
 		{

libfasta/fasta_header_parser.c

@@ -798,7 +798,7 @@ YY_RULE_SETUP
 								(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
 								strcpy(((*p_header)[*nbf]).value,header_yytext);
 										
-								p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
+								(*nbf)++;
 						  }
 	YY_BREAK
 case 3:
@@ -820,7 +820,7 @@ YY_RULE_SETUP
 case 5:
 YY_RULE_SETUP
 #line 69 "fasta_header_parser.l"
-{  // TODO
+{
 						/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",header_yytext);*/
 						if (i != 0)
 							field = store_in_field(field,header_yytext,&free_size,&i);
@@ -886,21 +886,24 @@ case YY_STATE_EOF(REGVAL):
 #line 113 "fasta_header_parser.l"
 {
 					field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-                    (*nbf)++;
+					p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
 					end_header_table(p_header, *nbf);
+					
 					free(field);
 					BEGIN(INITIAL);
                 	return 0;
                  }
 	YY_BREAK
 case YY_STATE_EOF(REGNAME):
-#line 122 "fasta_header_parser.l"
+#line 123 "fasta_header_parser.l"
 {
-						(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
+						/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
-						strcpy((*p_header)[*nbf].name,"definition");
+						strcpy((*p_header)[*nbf].name,"other_informations");
 						field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-                        (*nbf)++;
+						p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);						
-						end_header_table(p_header, nbf);
+						*/
+						end_header_table(p_header, *nbf);
+						
 						free(field);
 						BEGIN(INITIAL);
 						return 0;
@@ -908,10 +911,10 @@ case YY_STATE_EOF(REGNAME):
 	YY_BREAK
 case 12:
 YY_RULE_SETUP
-#line 133 "fasta_header_parser.l"
+#line 136 "fasta_header_parser.l"
 ECHO;
 	YY_BREAK
-#line 915 "<stdout>"
+#line 918 "<stdout>"
 case YY_STATE_EOF(INITIAL):
 case YY_STATE_EOF(REGID):
 	yyterminate();
@@ -1909,7 +1912,7 @@ void header_yyfree (void * ptr )
 
 #define YYTABLES_NAME "yytables"
 
-#line 133 "fasta_header_parser.l"
+#line 136 "fasta_header_parser.l"
 
 
 
@@ -1920,32 +1923,38 @@ int header_yywrap()
 
 element_from_header* header_parser_main(char *h)
 {
-	int nbfields, memory_allocated;
+	int nbfields,memory_allocated;
 	element_from_header* header;
 	char* nbfields_n;
-	YY_BUFFER_STATE state;
+	char* nbfields_v;
-    
+	
-    state=header_yy_scan_string(h);
+	nbfields_n = (char*) malloc(9*sizeof(char));
+	nbfields_v = (char*) malloc(5*sizeof(char));
 	
 	memory_allocated=MEMALLOCATED;
 	
-    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
-
-	nbfields_n = (char*) malloc(9*sizeof(char));
-	strcpy(nbfields_n, "nbfields");
-    header[0].name = nbfields_n;
-    
-    // Initialize memory to store the number of fields
-    header[0].value = (char*) malloc(10*sizeof(char));
-
 	nbfields=1;
 
+	strcpy(nbfields_n, "nbfields");
+	strcpy(nbfields_v, "1");
+
+    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
+    
+    header[0].name = nbfields_n;
+    header[0].value = nbfields_v;
+    
+	YY_BUFFER_STATE state;
+
+	state=header_yy_scan_string(h);
+
     header_parser(&nbfields, &memory_allocated, &header);
-    
+      
     header_yy_delete_buffer(state);
-    
+        
     return header;
 }
 
 
 
+
+

libfasta/fasta_header_parser.l

@@ -53,7 +53,7 @@ EQUAL				=
 								(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
 								strcpy(((*p_header)[*nbf]).value,yytext);
 										
-								p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
+								(*nbf)++;
 						  }
 
 
@@ -66,7 +66,7 @@ EQUAL				=
 						field = store_in_field(field,yytext,&free_size,&i);
 				    }
 
-<REGNAME>{SPACE}     {  // TODO
+<REGNAME>{SPACE}     {
 						/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",yytext);*/
 						if (i != 0)
 							field = store_in_field(field,yytext,&free_size,&i);
@@ -112,19 +112,22 @@ EQUAL				=
 
 <REGVAL><<EOF>>  {
 					field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-                    (*nbf)++;
+					p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
 					end_header_table(p_header, *nbf);
+					
 					free(field);
 					BEGIN(INITIAL);
                 	return 0;
                  }
 
 <REGNAME><<EOF>>      {
-						(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
+						/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
-						strcpy((*p_header)[*nbf].name,"definition");
+						strcpy((*p_header)[*nbf].name,"other_informations");
 						field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
-                        (*nbf)++;
+						p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);						
-						end_header_table(p_header, nbf);
+						*/
+						end_header_table(p_header, *nbf);
+						
 						free(field);
 						BEGIN(INITIAL);
 						return 0;
@@ -139,31 +142,37 @@ int header_yywrap()
 
 element_from_header* header_parser_main(char *h)
 {
-	int nbfields, memory_allocated;
+	int nbfields,memory_allocated;
 	element_from_header* header;
 	char* nbfields_n;
-	YY_BUFFER_STATE state;
+	char* nbfields_v;
-    
+	
-    state=yy_scan_string(h);
+	nbfields_n = (char*) malloc(9*sizeof(char));
+	nbfields_v = (char*) malloc(5*sizeof(char));
 	
 	memory_allocated=MEMALLOCATED;
 	
-    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
-
-	nbfields_n = (char*) malloc(9*sizeof(char));
-	strcpy(nbfields_n, "nbfields");
-    header[0].name = nbfields_n;
-    
-    // Initialize memory to store the number of fields
-    header[0].value = (char*) malloc(10*sizeof(char));
-
 	nbfields=1;
 
+	strcpy(nbfields_n, "nbfields");
+	strcpy(nbfields_v, "1");
+
+    header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
+    
+    header[0].name = nbfields_n;
+    header[0].value = nbfields_v;
+    
+	YY_BUFFER_STATE state;
+
+	state=yy_scan_string(h);
+
     header_parser(&nbfields, &memory_allocated, &header);
-    
+      
     yy_delete_buffer(state);
-    
+        
     return header;
 }
 
 
+
+

libfasta/fasta_seq_writer.c

@@ -52,7 +52,7 @@ void printOnlyHeaderFromTable(element_from_header* header, FILE* output)
 
 	fprintf(output,">%s ",header[1].value);
 
-	for (i = 2; i < nbf; i++)
+	for (i = 2; i <= nbf; i++)
 	{
 		if (strcmp(header[i].name, "definition") != 0)
 		{
@@ -60,10 +60,11 @@ void printOnlyHeaderFromTable(element_from_header* header, FILE* output)
 			fprintf(output,"=");
 		    fprintf(output,"%s; ",header[i].value);
 		}
-		else if (strcmp(header[i].name, "definition") == 0)
-			fprintf(output,"%s ", header[i].value);
 	}
 
+	if (strcmp(header[nbf].name, "definition") == 0)
+		fprintf(output,"%s; ",header[nbf].value);
+
 	fprintf(output,"\n");
 }
 

libfasta/header_mem_handler.c

@@ -76,7 +76,7 @@ element_from_header** check_and_realloc_mem_in_header_table(element_from_header*
 {
 	(*nbf)++;
 
-	if ((*nbf)+1 == *memory_allocated)
+	if (*nbf == *memory_allocated)
 	{
 		(*memory_allocated)++;
 		*p_header = (element_from_header*) realloc(*p_header, (*memory_allocated) * sizeof(element_from_header));
@@ -87,6 +87,7 @@ element_from_header** check_and_realloc_mem_in_header_table(element_from_header*
 
 void end_header_table(element_from_header** p_header, int nbf)
 {
-	*p_header = (element_from_header*) realloc(*p_header, nbf * sizeof(element_from_header));
+	nbf = nbf - 1;
+	//fprintf(stderr, "nbf = %d", nbf);
 	sprintf((*p_header)->value, "%d", nbf);
 }

libfasta/sequence.c

@@ -162,19 +162,24 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)
 {
 	char* seqTemp;
 	char c;
-	int32_t index = 0, seqIndex = 0, len = strlen(seq);
+	int32_t index = 1, seqIndex = 0, len = strlen(seq);
 	char* seqAlphabets = "acgtACGT";
 	int notAllATGC = 0;
+	int goOnParsing = 1;
 
 	seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
 
-	while (index < len)
+	while (goOnParsing)
 	{
 		c = seq[index++];
 		if (strchr(seqAlphabets, c) != NULL)
 			seqTemp[seqIndex++] = tolower(c);
+		else if (seq[index+1]=='\0')
+			goOnParsing = 0; // end of the sequence has been reached.
 		else if (c != '\n')
 			notAllATGC = 1;
+		if (index == len)
+			goOnParsing = 0;
 	}
 
 	if (notAllATGC)

libfile/Makefile

@@ -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) $@

liblcs/Makefile

@@ -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) $@

libsse/_sse.h

@@ -4,11 +4,16 @@
 #include <string.h>
 
 #include <inttypes.h>
-#ifdef __SSE2__
+
-#include <xmmintrin.h>
+#if defined(__SSE2__)
+#define USE_SSE2
+#elif defined(__ARM_NEON)
+#define USE_SSE2
+#include "sse2neon.h"
 #else
+// no SSE2 support, use emulation
 typedef long long __m128i __attribute__ ((__vector_size__ (16), __may_alias__));
-#endif /* __SSE2__ */
+#endif
 
 #ifndef MAX
 #define MAX(x,y) (((x)>(y)) ? (x):(y))
@@ -55,7 +60,7 @@ typedef union
 	} uint64_v;
 
 
-#ifdef __SSE2__
+#ifdef USE_SSE2
 
 static inline int8_t _s2_extract_epi8(__m128i r, const int p)
 {

libutils/Makefile

@@ -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) $@