From a7cd3be57070b5ce9c3e9f92f2c533d30c1436de Mon Sep 17 00:00:00 2001
From: Xian Chang <xhchang15@gmail.com>
Date: Tue, 2 Mar 2021 22:17:12 -0500
Subject: [PATCH 1/3] Add proper pairing tag to alignment message and gaf

---
 deps/vg.proto        | 1 +
 src/alignment_io.cpp | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/deps/vg.proto b/deps/vg.proto
index 827d76a..064d8f2 100644
--- a/deps/vg.proto
+++ b/deps/vg.proto
@@ -146,6 +146,7 @@ message Alignment {
     double time_used = 35; // The time this alignment took
     Position to_correct = 36; // A path/offset/orientation pair specifying the distance to the correct alignment
     bool correctly_mapped = 37; // This can be set to true to annotate the Alignment as having been mapped correctly.
+    bool properly_paired = 38;
     
     google.protobuf.Struct annotation = 100; // Annotations carried along with the Alignment.
 }
diff --git a/src/alignment_io.cpp b/src/alignment_io.cpp
index 88fd383..750f604 100644
--- a/src/alignment_io.cpp
+++ b/src/alignment_io.cpp
@@ -376,6 +376,12 @@ gafkluge::GafRecord alignment_to_gaf(function<size_t(nid_t)> node_to_length, fun
                 gaf.opt_fields["fp"] = make_pair("Z", aln.fragment_prev().name());
             }
         }
+
+        if (aln.properly_paired()) {
+            gaf.opt_fields["pd"] = make_pair("b", "1");
+        } else {
+            gaf.opt_fields["pd"] = make_pair("b", "0");
+        }
     }
 
     return gaf;    
@@ -515,6 +521,9 @@ void gaf_to_alignment(function<size_t(nid_t)> node_to_length, function<string(ni
         } else if (opt_it.first == "fn") {
             // get the fragment_next field
             aln.mutable_fragment_next()->set_name(opt_it.second.second);
+        } else if (opt_it.first == "pd") {
+            //Is this read properly paired
+            aln.set_properly_paired(opt_it.second.second == "1");
         }
     }
 }

From d0d39fda18f422ff5fbfbb2fe3a9a446a618ecf5 Mon Sep 17 00:00:00 2001
From: Xian Chang <xhchang15@gmail.com>
Date: Wed, 3 Mar 2021 11:18:09 -0500
Subject: [PATCH 2/3] Use an annotation for proper pairing instead of a
 separate field

---
 deps/vg.proto        |  1 -
 src/alignment_io.cpp | 15 ++++++++++-----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/deps/vg.proto b/deps/vg.proto
index 064d8f2..827d76a 100644
--- a/deps/vg.proto
+++ b/deps/vg.proto
@@ -146,7 +146,6 @@ message Alignment {
     double time_used = 35; // The time this alignment took
     Position to_correct = 36; // A path/offset/orientation pair specifying the distance to the correct alignment
     bool correctly_mapped = 37; // This can be set to true to annotate the Alignment as having been mapped correctly.
-    bool properly_paired = 38;
     
     google.protobuf.Struct annotation = 100; // Annotations carried along with the Alignment.
 }
diff --git a/src/alignment_io.cpp b/src/alignment_io.cpp
index 750f604..94f8f13 100644
--- a/src/alignment_io.cpp
+++ b/src/alignment_io.cpp
@@ -377,10 +377,12 @@ gafkluge::GafRecord alignment_to_gaf(function<size_t(nid_t)> node_to_length, fun
             }
         }
 
-        if (aln.properly_paired()) {
-            gaf.opt_fields["pd"] = make_pair("b", "1");
-        } else {
-            gaf.opt_fields["pd"] = make_pair("b", "0");
+        if (aln.has_annotation()) {
+            auto& annotation = aln.annotation();
+            if (annotation.fields().count("proper_pair")) {
+                bool is_properly_paired = (annotation.fields().at("proper_pair")).bool_value();
+            gaf.opt_fields["pd"] = make_pair("b", is_properly_paired ? "1" : "0");
+            }
         }
     }
 
@@ -523,7 +525,10 @@ void gaf_to_alignment(function<size_t(nid_t)> node_to_length, function<string(ni
             aln.mutable_fragment_next()->set_name(opt_it.second.second);
         } else if (opt_it.first == "pd") {
             //Is this read properly paired
-            aln.set_properly_paired(opt_it.second.second == "1");
+            auto* annotation = aln.mutable_annotation();
+            google::protobuf::Value is_properly_paired;
+            is_properly_paired.set_bool_value(opt_it.second.second == "1");
+            annotation->mutable_fields()->at("proper_pair") = is_properly_paired;
         }
     }
 }

From 34838033f95484152da2e80bf141e6ef0e65b67b Mon Sep 17 00:00:00 2001
From: Xian Chang <xhchang15@gmail.com>
Date: Wed, 3 Mar 2021 13:20:00 -0500
Subject: [PATCH 3/3] Set annotation value properly

---
 src/alignment_io.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/alignment_io.cpp b/src/alignment_io.cpp
index 94f8f13..fe26acf 100644
--- a/src/alignment_io.cpp
+++ b/src/alignment_io.cpp
@@ -528,7 +528,7 @@ void gaf_to_alignment(function<size_t(nid_t)> node_to_length, function<string(ni
             auto* annotation = aln.mutable_annotation();
             google::protobuf::Value is_properly_paired;
             is_properly_paired.set_bool_value(opt_it.second.second == "1");
-            annotation->mutable_fields()->at("proper_pair") = is_properly_paired;
+            (*annotation->mutable_fields())["proper_pair"] = is_properly_paired;
         }
     }
 }