From 21a972be84a43fc1113068240b6d63bf077fbf42 Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Thu, 6 Jul 2023 12:06:02 -0700 Subject: [PATCH] add integration test for scores --- test/t/15_vg_surject.t | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/t/15_vg_surject.t b/test/t/15_vg_surject.t index 70bfae0456d..6e0ddff37e2 100644 --- a/test/t/15_vg_surject.t +++ b/test/t/15_vg_surject.t @@ -6,7 +6,7 @@ BASH_TAP_ROOT=../deps/bash-tap PATH=../bin:$PATH # for vg -plan tests 46 +plan tests 47 vg construct -r small/x.fa >j.vg vg index -x j.xg j.vg @@ -36,7 +36,9 @@ is $(vg surject -p x -x x.xg -t 1 -s j.gam | grep -v "@" | cut -f3 | grep x | wc is $(vg surject -x x.xg -t 1 -s j.gam | grep -v "@" | cut -f3 | grep x | wc -l) \ 100 "vg surject doesn't need to be told which path to use" - + +is $(vg surject -x x.xg -t 1 -s x.gam | grep AS | wc -l) 100 "vg surject reports alignment scores" + vg paths -X -x x.vg | vg view -aj - | jq '.name = "sample#0#x#0"' | vg view -JGa - > paths.gam vg paths -X -x x.vg | vg view -aj - | jq '.name = "ref#0#x[55]"' | vg view -JGa - >> paths.gam vg augment x.vg -i paths.gam > x.aug.vg