From d8aeb7d0c5cdba555adf9e0e0729b4bf41ae22de Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Tue, 8 Aug 2023 11:45:30 -0400
Subject: [PATCH] fix tests again

---
 tests/t/chop.t  | 3 +--
 tests/t/merge.t | 8 ++++----
 2 files changed, 5 insertions(+), 6 deletions(-)

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..6b7a48d 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#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/human cat chimp/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 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#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/human cat chimp/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 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