fixed gcc4.6 errors, added --no-auto-append

src/ChangeLog

@@ -1,3 +1,7 @@
+[0.8.1]
+- added option to disable auto appending of DAA and DMND file extensions (--no-auto-append)
+- fixed some compiler errors for GCC 4.6
+
 [0.8.0]
 - fixed a bug that would sometimes cause alignments to be missed
 - fixed a bug that would cause alignments on the reverse strand to be missed in blastx mode

src/align/align_read.h

@@ -58,7 +58,7 @@ void align_read(Output_buffer &buffer,
 	const size_t db_letters = ref_header.letters;
 	unsigned padding[6];
 
-	typedef Map<typename vector<hit>::iterator,typename hit::template Query_id<1> > Map_t;
+	typedef Map<typename vector<hit>::iterator,typename hit::Query_id<1> > Map_t;
 	Map_t hits (begin, end);
 	typename Map_t::Iterator i = hits.begin();
 	while(i.valid()) {

src/basic/basic.cpp

@@ -4,7 +4,7 @@
 #include "translate.h"
 #include "statistics.h"
 
-const char* Const::version_string = "0.8.0";
+const char* Const::version_string = "0.8.1";
 const char* Const::program_name = "diamond";
 const char* Const::id_delimiters = " \a\b\f\n\r\t\v";
 

src/basic/config.cpp

@@ -82,7 +82,8 @@ Config::Config(int argc, const char **argv)
 		("index-mode", 0, "index mode (0=4x12, 1=16x9)", index_mode)
 		("fetch-size", 0, "trace point fetch size", fetch_size, 4096u)
 		("single-domain", 0, "Discard secondary domains within one target sequence", single_domain)
-		("dbsize", 0, "effective database size (in letters)", db_size);
+		("dbsize", 0, "effective database size (in letters)", db_size)
+		("no-auto-append", 0, "disable auto appending of DAA and DMND file extensions", no_auto_append);
 
 	Options_group view_options("View options");
 	view_options.add()
@@ -154,8 +155,10 @@ Config::Config(int argc, const char **argv)
 		set_option(index_mode, 0u);
 	}
 
-	auto_append_extension(database, ".dmnd");
-	auto_append_extension(daa_file, ".daa");
+	if (!no_auto_append) {
+		auto_append_extension(database, ".dmnd");
+		auto_append_extension(daa_file, ".daa");
+	}
 
 	message_stream << Const::program_name << " v" << Const::version_string << "." << Const::build_version << " | by Benjamin Buchfink <[email protected]>" << endl; 
 	message_stream << "Check http://github.com/bbuchfink/diamond/releases for updates." << endl << endl;

src/basic/config.h

@@ -66,6 +66,7 @@ struct Config
 
 	bool		mode_sensitive;
 	unsigned	verbosity;
+	bool no_auto_append;
 
 	typedef enum { makedb = 0, blastp = 1, blastx = 2, view = 3, help = 4, version = 5 } Command;
 	unsigned	command;

src/basic/const.h

@@ -25,7 +25,7 @@ struct Const
 {
 
 	enum {
-		build_version = 62,
+		build_version = 63,
 		build_compatibility = 52,
 		db_version = 0,
 		daa_version = 0,

src/dp/score_vector.h

@@ -55,7 +55,7 @@ struct score_vector<uint8_t>
 		data_ = _mm_set1_epi8(score_traits<uint8_t>::zero);
 	}
 
-	explicit score_vector(int x):
+	explicit score_vector(char x):
 		data_ (_mm_set(x))
 	{ }
 

src/util/strict_fstream.hpp

@@ -58,7 +58,7 @@ struct static_method_holder
                 "binary"
             };
         std::string res;
-        for (size_t i = 0; i < n_modes; ++i)
+        for (size_t i = 0; i < (size_t)n_modes; ++i)
         {
             if (mode & mode_val_v[i])
             {

src/util/util.h

@@ -254,19 +254,10 @@ inline string* get_str(const char *s, const char *delimiters)
 	return new string (s, find_first_of(s, delimiters));
 }
 
-inline __m128i _mm_set(int a)
+inline __m128i _mm_set(char a)
 {
-	int y = a << 8 | a;
-	__m128i z = __m128i();
-	z = _mm_insert_epi16 (z, y, 0);
-	z = _mm_insert_epi16 (z, y, 1);
-	z = _mm_insert_epi16 (z, y, 2);
-	z = _mm_insert_epi16 (z, y, 3);
-	z = _mm_insert_epi16 (z, y, 4);
-	z = _mm_insert_epi16 (z, y, 5);
-	z = _mm_insert_epi16 (z, y, 6);
-	z = _mm_insert_epi16 (z, y, 7);
-	return z;
+	const int x = (int)a;
+	return _mm_set1_epi32(x << 24 | x << 16 | x << 8 | x);
 }
 
 template<typename _t, unsigned d1, unsigned d2>