Fixed LTO issue, ppos output fields in realign.

src/ChangeLog

@@ -23,6 +23,10 @@
   `--iterate` option to activate linear-time feature.
 - Added the option `--linsearch` to activate linear-time feature for the search
   workflows.
+- Fixed a bug that caused the `ppos` and `positive` output fields not to work
+  for the `realign` workflow.
+- Fixed an issue that caused motif masking not to work when compiled with link
+  time optimization.
 
 [2.1.1]
 - Fixed compilation errors on non-x86 systems and for the clang compiler.

src/basic/match.h

@@ -451,6 +451,7 @@ struct TypeSerializer<HspContext> {
 		buf_->write(h.subject_len);
 		buf_->write(h.identities());
 		buf_->write(h.mismatches());
+		buf_->write(h.positives());
 		buf_->write(h.gaps());
 		buf_->write(h.length());
 		buf_->write(h.gap_openings());
@@ -488,6 +489,7 @@ struct TypeDeserializer<HspContext> {
 		file_->read(h.subject_len);
 		file_->read(h.hsp_.identities);
 		file_->read(h.hsp_.mismatches);
+		file_->read(h.hsp_.positives);
 		file_->read(h.hsp_.gaps);
 		file_->read(h.hsp_.length);
 		file_->read(h.hsp_.gap_openings);

src/masking/masking.h

@@ -103,4 +103,5 @@ struct MaskingTable {
 };
 
 const size_t MOTIF_LEN = 8;
-extern const std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table;
+extern std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table;
+void init_motif_table();

src/masking/motifs.cpp

@@ -1,6 +1,8 @@
 #include "masking.h"
 
-const std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table = {
+std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table;
+
+static const char motif_strings[][9] = {
 "FRKYTAFT",
 "KYTAFTIP",
 "RKYTAFTI",
@@ -8001,4 +8003,11 @@ const std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table = {
 "EYRLYLDA",
 "YRLYLDAY",
 "QFHQKLLK",*/
-};
+};
+
+void init_motif_table() {
+	const auto n = sizeof(motif_strings) / sizeof(motif_strings[0]);
+	motif_table.reserve(n);
+	for (size_t i = 0; i < n; ++i)
+		motif_table.insert(motif_strings[i]);
+}

src/run/main.cpp

@@ -90,6 +90,7 @@ namespace Incremental {
 int main(int ac, const char* av[])
 {
 	try {
+		init_motif_table();
 		CommandLineParser parser;
 		config = Config(ac, av, true, parser);