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add integration test for scores
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@jeizenga
jeizenga committed Jul 6, 2023
1 parent f8cf5f1 commit 21a972b
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6 changes: 4 additions & 2 deletions test/t/15_vg_surject.t
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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@adamnovak
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vg CI tests complete for branch surject-score. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 21399 seconds

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