Actualiser libsse/_sse.h

Makefile

@@ -1,3 +1,4 @@
+PREFIX=/usr/local
 
 SOURCES = libfasta/fasta_header_parser.c \
 		  libfasta/fasta_seq_writer.c \
@@ -44,3 +45,12 @@ $(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
+

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)

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)
 {