From 4276e7469c21204ab5c6605129a5f4095eeb4613 Mon Sep 17 00:00:00 2001
From: Benjamin Buchfink <buchfink@gmail.com>
Date: Mon, 20 Feb 2023 10:57:47 +0100
Subject: [PATCH] Fixed LTO issue, ppos output fields in realign.

---
 src/ChangeLog          |  4 ++++
 src/basic/match.h      |  2 ++
 src/masking/masking.h  |  3 ++-
 src/masking/motifs.cpp | 13 +++++++++++--
 src/run/main.cpp       |  1 +
 5 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/src/ChangeLog b/src/ChangeLog
index b0d150e2..f7399b86 100644
--- a/src/ChangeLog
+++ b/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.
diff --git a/src/basic/match.h b/src/basic/match.h
index b5e6f4dd..4401e9c5 100644
--- a/src/basic/match.h
+++ b/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);
diff --git a/src/masking/masking.h b/src/masking/masking.h
index 0010834a..f972675d 100644
--- a/src/masking/masking.h
+++ b/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;
\ No newline at end of file
+extern std::unordered_set<Kmer<MOTIF_LEN>, Kmer<MOTIF_LEN>::Hash> motif_table;
+void init_motif_table();
\ No newline at end of file
diff --git a/src/masking/motifs.cpp b/src/masking/motifs.cpp
index b1e7edc8..e278e977 100644
--- a/src/masking/motifs.cpp
+++ b/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",*/
-};
\ No newline at end of file
+};
+
+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]);
+}
\ No newline at end of file
diff --git a/src/run/main.cpp b/src/run/main.cpp
index 840ac412..c06308dd 100644
--- a/src/run/main.cpp
+++ b/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);