just use underscore for names

halMergeChroms.cpp

@@ -33,13 +33,9 @@ static void initParser(CLParser* optionsParser) {
 }
 
 // we expect to see the same ancestor sequence names in multiple input files. we uniqify them by adding
-// .i to them where i is the file's position in the input.
+// _i to them where i is the file's position in the input.
 static string anc_seq_name(const string& seq_name, size_t idx) {
-    return seq_name + ".hmc" + to_string(idx);
-}
-// undo the above
-static string orig_seq_name(const string& seq_name) {
-    return seq_name.substr(0, seq_name.rfind(".hmc"));
+    return seq_name + "_" + to_string(idx);
 }
 
 // get the dimensions from all genomes in all input files

tests/t/merge.t

@@ -27,8 +27,8 @@ hal2vg small2.hal | vg mod -O - | vg ids -s - > small2.vg
 hal2vg merged1.hal | vg mod -O - | vg ids -s - > merged1.vg
 vg view small.vg | sort > small.gfa
 vg view small2.vg | sort > small2.gfa
-vg find -x merged1.vg -p cat.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/.hmc0//g' | sed -e 's/.hmc1//g' > merged1.comp1.gfa
-vg find -x merged1.vg -p cow.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/.hmc0//g' | sed -e 's/.hmc1//g' > merged1.comp2.gfa
+vg find -x merged1.vg -p cat.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' > merged1.comp1.gfa
+vg find -x merged1.vg -p cow.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' > merged1.comp2.gfa
 diff small.gfa merged1.comp1.gfa
 is $? 0 "First component of merged graph identical to first input graph"
 diff small2.gfa merged1.comp2.gfa
@@ -60,8 +60,8 @@ hal2vg small2.hal | vg mod -O - | vg ids -s - > small2.vg
 hal2vg merged1.hal | vg mod -O - | vg ids -s - > merged1.vg
 vg view small.vg | sort > small.gfa
 vg view small2.vg | sort > small2.gfa
-vg find -x merged1.vg -p cat.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/.hmc0//g' | sed -e 's/.hmc1//g' > merged1.comp1.gfa
-vg find -x merged1.vg -p cow.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/.hmc0//g' | sed -e 's/.hmc1//g' > merged1.comp2.gfa
+vg find -x merged1.vg -p cat.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' > merged1.comp1.gfa
+vg find -x merged1.vg -p cow.3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' > merged1.comp2.gfa
 diff small.gfa merged1.comp1.gfa
 is $? 0 "First component of merged graph identical to first input graph"
 diff small2.gfa merged1.comp2.gfa