From 8ceb4cd678b36cc383675673e62cbd6bfb182733 Mon Sep 17 00:00:00 2001
From: Jordan Eizenga <joeizeng@gmail.com>
Date: Thu, 1 Aug 2024 13:37:48 -0700
Subject: [PATCH] bugfix invalid surjected alignments

---
 src/multipath_alignment.cpp       |  8 ++++++++
 src/multipath_alignment_graph.cpp | 11 ++++++-----
 src/surjector.cpp                 |  6 ++++++
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/multipath_alignment.cpp b/src/multipath_alignment.cpp
index d91ae71a03a..7d7679c15d2 100644
--- a/src/multipath_alignment.cpp
+++ b/src/multipath_alignment.cpp
@@ -3857,6 +3857,14 @@ namespace vg {
 #endif
                     return false;
                 }
+                for (const auto& connection : subpath.connection()) {
+                    if (connection.next() <= i) {
+#ifdef debug_verbose_validation
+                        cerr << "validation failure on connection topological order" << endl;
+#endif
+                        return false;
+                    }
+                }
             }
         }
         
diff --git a/src/multipath_alignment_graph.cpp b/src/multipath_alignment_graph.cpp
index ce36787a12c..a43a7a2722c 100644
--- a/src/multipath_alignment_graph.cpp
+++ b/src/multipath_alignment_graph.cpp
@@ -6170,17 +6170,17 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
                 if (aligning_tail_length < tail_length) {
                     // Tail is too long. Just make a softclip directly in the base graph ID space.
                     // TODO: What if we just don't produce this? Do we get softclips for free?
+                    
+                    size_t cut_point = (path_node.end - alignment.sequence().begin()) + aligning_tail_length;
+                    size_t tail_remaining = tail_length - aligning_tail_length;
 #ifdef debug_multipath_alignment
                     cerr << "softclip long right" << endl;
 #endif
-                    size_t cut_point = (path_node.end - alignment.sequence().begin()) + aligning_tail_length;
-                    size_t tail_remaining = tail_length - aligning_tail_length;
                     
                     for (auto& alt_aln : alt_alignments) {
-                                                
                         alt_aln.mutable_sequence()->append(alignment.sequence(), cut_point, tail_remaining);
                         if (!alt_aln.quality().empty()) {
-                            alt_aln.mutable_sequence()->append(alignment.quality(), cut_point, tail_remaining);
+                            alt_aln.mutable_quality()->append(alignment.quality(), cut_point, tail_remaining);
                         }
                         
                         Mapping* mapping = alt_aln.mutable_path()->mutable_mapping(alt_aln.path().mapping_size() - 1);
@@ -6188,6 +6188,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
                         if (final_edit->from_length() == 0 && !final_edit->sequence().empty()) {
                             // extend the softclip
                             final_edit->set_sequence(final_edit->sequence() + alignment.sequence().substr(cut_point, tail_remaining));
+                            final_edit->set_to_length(final_edit->sequence().size());
                         }
                         else {
                             final_edit = mapping->add_edit();
@@ -6342,7 +6343,7 @@ void MultipathAlignmentGraph::align(const Alignment& alignment, const HandleGrap
                             
                             alt_aln.mutable_sequence()->append(alignment.sequence(), 0, tail_remaining);
                             if (!alt_aln.quality().empty()) {
-                                alt_aln.mutable_sequence()->append(alignment.quality(), 0, tail_remaining);
+                                alt_aln.mutable_quality()->append(alignment.quality(), 0, tail_remaining);
                             }
                             
                             Mapping* mapping = alt_aln.mutable_path()->mutable_mapping(0);
diff --git a/src/surjector.cpp b/src/surjector.cpp
index b428397223a..e7a59e2615e 100644
--- a/src/surjector.cpp
+++ b/src/surjector.cpp
@@ -4240,7 +4240,13 @@ using namespace std;
                                 auto mappings = path_chunk.second.mutable_mapping();
                                 mappings->erase(mappings->begin(), mappings->begin() + mappings_to_delete);
                                 auto edits = mappings->front().mutable_edit();
+                                size_t deleting_from_length = 0;
+                                for (size_t e = 0; e < edits_to_delete; ++e) {
+                                    deleting_from_length += (*edits)[e].from_length();
+                                }
                                 edits->erase(edits->begin(), edits->begin() + edits_to_delete);
+                                auto position = mappings->front().mutable_position();
+                                position->set_offset(position->offset() + deleting_from_length);
                                 
                                 // trim ref interval
                                 for (size_t m = 0; m < mappings_to_delete; ++m) {