From df5a5a4e6faea39e470ec8bc629c152248e41219 Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Wed, 2 Aug 2023 13:44:34 -0400
Subject: [PATCH 1/2] always set haplotype for refsense -- vg 1.50.0 requires
 it

---
 hal2vg.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hal2vg.cpp b/hal2vg.cpp
index 0e9e623..6910add 100644
--- a/hal2vg.cpp
+++ b/hal2vg.cpp
@@ -653,7 +653,7 @@ void pinch_to_handle(const Genome* genome,
         subrange_t subpath = resolve_subpath_naming(parsed_name);
         string parsed_genome_name = genome->getName();
         size_t haplotype = resolve_haplotype_naming(parsed_genome_name);
-        if (sense == PathSense::HAPLOTYPE && haplotype == PathMetadata::NO_HAPLOTYPE) {
+        if (haplotype == PathMetadata::NO_HAPLOTYPE) {
             haplotype = 0;
         }
         // create the path

From 4d177ac7fc02faae5e718fe71c6bd12161ecfc70 Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Wed, 2 Aug 2023 14:41:33 -0400
Subject: [PATCH 2/2] fix tests

---
 tests/small/truth.json | 6 +++---
 tests/t/chop.t         | 3 +--
 tests/t/merge.t        | 8 ++++----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/tests/small/truth.json b/tests/small/truth.json
index 52e8e81..aa298a9 100644
--- a/tests/small/truth.json
+++ b/tests/small/truth.json
@@ -173,7 +173,7 @@
           "rank": "6"
         }
       ],
-      "name": "cat#3"
+      "name": "cat#0#3"
     },
     {
       "mapping": [
@@ -264,7 +264,7 @@
           "rank": "7"
         }
       ],
-      "name": "chimp#2"
+      "name": "chimp#0#2"
     },
     {
       "mapping": [
@@ -368,7 +368,7 @@
           "rank": "8"
         }
       ],
-      "name": "human#1"
+      "name": "human#0#1"
     }
   ]
 }
diff --git a/tests/t/chop.t b/tests/t/chop.t
index 2e13bf5..bf527f9 100644
--- a/tests/t/chop.t
+++ b/tests/t/chop.t
@@ -8,8 +8,7 @@ PATH=../deps/hal:$PATH
 
 plan tests 18
 
-#vg convert -g chop/tiny-flat.gfa -p > tiny-flat.vg
-vg convert -g chop/tiny-flat.gfa -o > tiny-flat.vg
+vg convert -g chop/tiny-flat.gfa -p > tiny-flat.vg
 printf "x\t0\t100\n" > all.bed
 clip-vg tiny-flat.vg -b all.bed | vg view - | grep -v ^H > chopped-all.gfa
 is "$(cat chopped-all.gfa | wc -l)" 0 "chopping everything clears out the graph"
diff --git a/tests/t/merge.t b/tests/t/merge.t
index 0ef503d..86622b9 100644
--- a/tests/t/merge.t
+++ b/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/_0//g' | sed -e 's/_1//g' | sed -e "s/cat human chimp/human chimp cat/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' | sed -e "s/human chimp cow/cow human chimp/g" > merged1.comp2.gfa
+vg find -x merged1.vg -p cat#0#3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' | sed -e "s/human chimp cat/chimp human cat/g" > merged1.comp1.gfa
+vg find -x merged1.vg -p cow#0#3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' | sed -e "s/human cow chimp/chimp human cow/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/_0//g' | sed -e 's/_1//g' | sed -e "s/cat human chimp/human chimp cat/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' | sed -e "s/human chimp cow/cow human chimp/g" > merged1.comp2.gfa
+vg find -x merged1.vg -p cat#0#3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' | sed -e "s/human chimp cat/chimp human cat/g" > merged1.comp1.gfa
+vg find -x merged1.vg -p cow#0#3:1 -c 1000 | vg ids -s - | vg view - | sort | sed -e 's/_0//g' | sed -e 's/_1//g' | sed -e "s/human cow chimp/chimp human cow/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