bugfix invalid surjected alignments

vgteam · Aug 1, 2024 · 8ceb4cd · 8ceb4cd · adamnovak · Aug 1, 2024
1 parent 2761ced
commit 8ceb4cd
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Showing 3 changed files with 20 additions and 5 deletions.
diff --git 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
@@ -6170,24 +6170,25 @@ 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);
                         Edit* final_edit = mapping->mutable_edit(mapping->edit_size() - 1);
                         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
@@ -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) {