From d804de66130cda6d7010acbd1f1fe8495e27c3f4 Mon Sep 17 00:00:00 2001
From: "Dr. K. D. Murray" <1560490+kdm9@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:16:37 +0200
Subject: [PATCH 1/2] fix: invalid paf produced for some patch alignments

---
 src/common/wflign/src/wflign_patch.cpp | 43 ++++++++++++++------------
 1 file changed, 23 insertions(+), 20 deletions(-)

diff --git a/src/common/wflign/src/wflign_patch.cpp b/src/common/wflign/src/wflign_patch.cpp
index 6eae79e6..9bfad249 100644
--- a/src/common/wflign/src/wflign_patch.cpp
+++ b/src/common/wflign/src/wflign_patch.cpp
@@ -2032,26 +2032,29 @@ query_start : query_end)
         // write how many reverse complement alignments were found
         //std::cerr << "got " << rev_patch_alns.size() << " rev patch alns" << std::endl;
         for (auto& patch_aln : multi_patch_alns) {
-            write_alignment_paf(
-                out,
-                patch_aln,
-                query_name,
-                query_total_length,
-                query_offset,
-                query_length,
-                query_is_rev,
-                target_name,
-                target_total_length,
-                target_offset,
-                target_length,
-                min_identity,
-                mashmap_estimated_identity,
-                false,  // Don't add an endline after each alignment
-                true);  // This is a reverse complement alignment
-            // write tag indicating that this is a multipatch alignment
-            out << "\t" << "pt:Z:true" << "\t"
-                // and if the patch is inverted as well
-                << "\t" << "iv:Z:" << (patch_aln.is_rev ? "true" : "false") << "\n";
+            if (patch_aln.ok) {
+                // write_alignment_paf only writes anything if aln.ok. We need to guard the manual tag writing below with the same conditional to avoid writing an invalid PAF.
+                write_alignment_paf(
+                    out,
+                    patch_aln,
+                    query_name,
+                    query_total_length,
+                    query_offset,
+                    query_length,
+                    query_is_rev,
+                    target_name,
+                    target_total_length,
+                    target_offset,
+                    target_length,
+                    min_identity,
+                    mashmap_estimated_identity,
+                    false,  // Don't add an endline after each alignment
+                    true);  // This is a reverse complement alignment
+                // write tag indicating that this is a multipatch alignment
+                out << "\t" << "pt:Z:true" << "\t"
+                    // and if the patch is inverted as well
+                    << "iv:Z:" << (patch_aln.is_rev ? "true" : "false") << "\n";
+            }
         }
     }
     out << std::flush;

From dd0bbc3b576c141e9021b9c64cfdc4dd75e51c28 Mon Sep 17 00:00:00 2001
From: "Dr. K.D. Murray" <foss@kdmurray.id.au>
Date: Tue, 24 Sep 2024 16:07:13 +0200
Subject: [PATCH 2/2] properly detect if a paf line was written

---
 src/common/wflign/src/wflign_patch.cpp | 11 +++++++----
 src/common/wflign/src/wflign_patch.hpp |  2 +-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/common/wflign/src/wflign_patch.cpp b/src/common/wflign/src/wflign_patch.cpp
index 9bfad249..817250a8 100644
--- a/src/common/wflign/src/wflign_patch.cpp
+++ b/src/common/wflign/src/wflign_patch.cpp
@@ -2032,9 +2032,8 @@ query_start : query_end)
         // write how many reverse complement alignments were found
         //std::cerr << "got " << rev_patch_alns.size() << " rev patch alns" << std::endl;
         for (auto& patch_aln : multi_patch_alns) {
-            if (patch_aln.ok) {
-                // write_alignment_paf only writes anything if aln.ok. We need to guard the manual tag writing below with the same conditional to avoid writing an invalid PAF.
-                write_alignment_paf(
+            // write_alignment_paf only writes anything if aln.ok. We need to guard the manual tag writing below with the same conditional to avoid writing an invalid PAF.
+            bool wrote = write_alignment_paf(
                     out,
                     patch_aln,
                     query_name,
@@ -2050,6 +2049,7 @@ query_start : query_end)
                     mashmap_estimated_identity,
                     false,  // Don't add an endline after each alignment
                     true);  // This is a reverse complement alignment
+            if (wrote) {
                 // write tag indicating that this is a multipatch alignment
                 out << "\t" << "pt:Z:true" << "\t"
                     // and if the patch is inverted as well
@@ -2224,7 +2224,7 @@ void write_alignment_sam(
     free(patch_cigar);
 }
 
-void write_alignment_paf(
+bool write_alignment_paf(
         std::ostream& out,
         const alignment_t& aln,
         const std::string& query_name,
@@ -2240,6 +2240,7 @@ void write_alignment_paf(
         const float& mashmap_estimated_identity,
         const bool& with_endline,
         const bool& is_rev_patch) {
+    bool ret = false;  // return true if we wrote the alignment
 
     if (aln.ok) {
         uint64_t matches = 0;
@@ -2294,9 +2295,11 @@ void write_alignment_paf(
             if (with_endline) {
                 out << std::endl;
             }
+            ret = true;
         }
         free(cigar);
     }
+    return ret;
 }
 
 double float2phred(const double& prob) {
diff --git a/src/common/wflign/src/wflign_patch.hpp b/src/common/wflign/src/wflign_patch.hpp
index 80530a54..7e197abb 100644
--- a/src/common/wflign/src/wflign_patch.hpp
+++ b/src/common/wflign/src/wflign_patch.hpp
@@ -144,7 +144,7 @@ namespace wflign {
             const char* query,
             const char* target,
             const int64_t& target_pointer_shift);
-        void write_alignment_paf(
+        bool write_alignment_paf(
                 std::ostream& out,
                 const alignment_t& aln,
                 const std::string& query_name,