Make sure GAMP surjection detects when you have the wrong graph

src/subcommand/surject_main.cpp

@@ -76,6 +76,27 @@ static void ensure_alignment_is_for_graph(const Alignment& aln, const HandleGrap
     }
 }
 
+/// If the given multipath alignment doesn't make sense against the given graph (i.e.
+/// doesn't agree with the nodes in the graph), print a message and stop the
+/// program. Is thread-safe.
+static void ensure_alignment_is_for_graph(const MultipathAlignment& aln, const HandleGraph& graph) {
+    // For multipaht alignments we just check node existence.
+    for (auto& subpath : aln.subpath()) {
+        for (auto& mapping : subpath.path().mapping()) {
+            nid_t node_id = mapping.position().node_id();
+            if (!graph.has_node(node_id)) {
+                // Something is wrong with this alignment.
+                #pragma omp critical (cerr)
+                {
+                    std::cerr << "error:[vg surject] MultipathAlignment " << aln.name() << " cannot be interpreted against this graph: node " << node_id << " does not exist!" << std::endl;
+                    std::cerr << "Make sure that you are using the same graph that the reads were mapped to!" << std::endl;
+                }
+                exit(1);
+            }
+        }
+    }
+}
+
 int main_surject(int argc, char** argv) {
 
     if (argc == 2) {
@@ -554,6 +575,11 @@ int main_surject(int argc, char** argv) {
 
                             exit(1);
                         }
+
+                        if (validate) {
+                            ensure_alignment_is_for_graph(src1, *xgidx);
+                            ensure_alignment_is_for_graph(src2, *xgidx);
+                        }
 
                         // convert out of protobuf
                         multipath_alignment_t mp_src1, mp_src2;
@@ -661,6 +687,10 @@ int main_surject(int argc, char** argv) {
                             watchdog->check_in(thread_num, src.name());
                         }
 
+                        if (validate) {
+                            ensure_alignment_is_for_graph(src, *xgidx);
+                        }
+
                         multipath_alignment_t mp_src;
                         from_proto_multipath_alignment(src, mp_src);
 

src/surjector.hpp

@@ -24,7 +24,14 @@
 namespace vg {
 
 using namespace std;
-
+
+    /**
+     * Widget to surject alignments down to linear paths in the graph.
+     *
+     * Assumes the alignments actually go with the graph; the caller is
+     * repsonsible for ensuring that e.g. all nodes referenced by the
+     * alignments actually exist.
+     */
     class Surjector : public AlignerClient {
     public:
 

test/t/15_vg_surject.t

@@ -6,7 +6,7 @@ BASH_TAP_ROOT=../deps/bash-tap
 PATH=../bin:$PATH # for vg
 
 
-plan tests 48
+plan tests 52
 
 vg construct -r small/x.fa >j.vg
 vg index -x j.xg j.vg
@@ -196,7 +196,15 @@ is "$(vg surject -x x.xg -s -m -t 1 mapped.gamp | grep -v '@' | wc -l)" 40 "GAMP
 is "$(vg surject -x x.xg -M -m -s -t 1 mapped.gamp | grep -v '@' | wc -l)" 80 "GAMP surject can return multimappings"
 is "$(vg surject -x x.xg -M -m -s -i -t 1 mapped.gamp | grep -v '@' | wc -l)" 80 "GAMP surject can return multimappings"
 
-rm x.vg x.pathdup.vg x.xg x.gcsa x.gcsa.lcp x.gam mapped.gam mapped.gamp
+vg construct -r tiny/tiny.fa > tiny.vg
+vg surject -x tiny.vg -s -t 1 mapped.gam >/dev/null 2>err.txt
+is "${?}" "1" "Surjection fails when using the wrong graph for GAM"
+is "$(cat err.txt | grep 'cannot be interpreted' | wc -l)" "1" "Surjection of GAM to the wrong graph reports the problem"
+vg surject -x tiny.vg -s -t 1 -m mapped.gamp >/dev/null 2>err.txt
+is "${?}" "1" "Surjection fails when using the wrong graph for GAMP"
+is "$(cat err.txt | grep 'cannot be interpreted' | wc -l)" "1" "Surjection of GAMP to the wrong graph reports the problem"
+
+rm x.vg x.pathdup.vg x.xg x.gcsa x.gcsa.lcp x.gam mapped.gam mapped.gamp tiny.vg err.txt
 
 is "$(vg surject -p CHM13#0#chr8 -x surject/opposite_strands.gfa --prune-low-cplx --sam-output --gaf-input surject/opposite_strands.gaf | grep -v "^@" | cut -f3-12 | sort | uniq | wc -l)" "1" "vg surject low compelxity pruning gets the same alignment regardless of read orientation"