Merge branch 'dnanexus-rnd-mlin-find-remove-orphans'

vgteam · Aug 25, 2015 · e3c2ba8 · e3c2ba8
2 parents bb981cc + 17ebaa7
commit e3c2ba8
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/main.cpp b/main.cpp
@@ -1931,6 +1931,7 @@ int main_find(int argc, char** argv) {
             if (context_size > 0) {
                 vindex.expand_context(graph, context_size);
             }
+            graph.remove_orphan_edges();
             graph.serialize_to_ostream(cout);
         }
         if (!range.empty()) {

diff --git a/test/t/05_vg_find.t b/test/t/05_vg_find.t
@@ -5,7 +5,7 @@ BASH_TAP_ROOT=../bash-tap
 
 PATH=..:$PATH # for vg
 
-plan tests 15
+plan tests 16
 
 vg construct -r small/x.fa -v small/x.vcf.gz >x.vg
 is $? 0 "construction"
@@ -29,10 +29,12 @@ is $(vg find -S AGGGCTTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT x.vg | v
 
 is $(vg find -S AGGGCTTTTAACTACTCCACATCCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT -j 11 x.vg | vg view - | wc -l) 33 "vg find returns a correctly-sized graph when using jump-kmers"
 
-is $(vg find -p x:0-100 x.vg | vg view -g - | wc -l) 58 "vg find returns a subgraph corresponding to particular reference coordinates"
+is $(vg find -p x:0-100 x.vg | vg view -g - | wc -l) 42 "vg find returns a subgraph corresponding to particular reference coordinates"
 
 is $(vg find -p x:0-100 x.vg | vg view -j - | jq ".node[].sequence" | tr -d '"\n' | wc -c) 100 "vg find returns a path of the correct length"
 
+is $(vg find -p x:0-100 -c 1 x.vg | vg view -g - | wc -l) 70 "larger graph is returned when the reference path is queried with context"
+
 is $(vg find -p x -c 10 x.vg | vg view -g - | wc -l) $(vg view -g x.vg | wc -l) "entire graph is returned when the reference path is queried with context"
 
 is $(vg find -s 10 x.vg | wc -l) 1 "we can find edges on start"