From f8cf5f112a3d202013746f9feac966ee5dcdcfe1 Mon Sep 17 00:00:00 2001
From: Jordan Eizenga <joeizeng@gmail.com>
Date: Thu, 6 Jul 2023 11:48:54 -0700
Subject: [PATCH] report alignment scores from surject

---
 src/alignment.cpp                   | 6 ++++++
 src/multipath_alignment_emitter.cpp | 5 ++++-
 src/subcommand/convert_main.cpp     | 2 +-
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/src/alignment.cpp b/src/alignment.cpp
index 633deea2888..665a84b03f8 100644
--- a/src/alignment.cpp
+++ b/src/alignment.cpp
@@ -805,6 +805,12 @@ bam1_t* alignment_to_bam_internal(bam_hdr_t* header,
         }
     }
     
+    if (~core.flag & BAM_FUNMAP) {
+        // we've decided that it is aligned
+        int32_t score = alignment.score();
+        bam_aux_append(bam, "AS", 'i', sizeof(int32_t), (uint8_t*) &score);
+    }
+    
     if (!alignment.read_group().empty()) {
         bam_aux_append(bam, "RG", 'Z', alignment.read_group().size() + 1, (uint8_t*) alignment.read_group().c_str());
     }
diff --git a/src/multipath_alignment_emitter.cpp b/src/multipath_alignment_emitter.cpp
index 1d7ef25a610..705910b1dff 100644
--- a/src/multipath_alignment_emitter.cpp
+++ b/src/multipath_alignment_emitter.cpp
@@ -337,10 +337,13 @@ void MultipathAlignmentEmitter::create_alignment_shim(const string& name, const
             mapped = true;
         }
     }
-    // hacky way to inform the conversion code that the read is mapped
     if (mapped) {
+        // hacky way to inform the conversion code that the read is mapped
         shim.mutable_path()->add_mapping();
+        // and we'll also communicate the alignment score
+        shim.set_score(optimal_alignment_score(mp_aln, true));
     }
+    
     // this tag comes from surject and is used in both
     if (mp_aln.has_annotation("all_scores")) {
         auto anno = mp_aln.get_annotation("all_scores");
diff --git a/src/subcommand/convert_main.cpp b/src/subcommand/convert_main.cpp
index 3d6bb0c9b7f..710bdb4458a 100644
--- a/src/subcommand/convert_main.cpp
+++ b/src/subcommand/convert_main.cpp
@@ -187,7 +187,7 @@ int main_convert(int argc, char** argv) {
             {
                 num_threads = parse<int>(optarg);
                 if (num_threads <= 0) {
-                    cerr << "error:[vg mpmap] Thread count (-t) set to " << num_threads << ", must set to a positive integer." << endl;
+                    cerr << "error:[vg convert] Thread count (-t) set to " << num_threads << ", must set to a positive integer." << endl;
                     exit(1);
                 }
                 omp_set_num_threads(num_threads);