Skip to content

Commit

Permalink
Use correct target score for having full length bonus
Browse files Browse the repository at this point in the history
  • Loading branch information
adamnovak committed May 6, 2024
1 parent d9487ef commit 5dc1f7d
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion test/t/50_vg_giraffe.t
Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ vg index -j 1mb1kgp.dist 1mb1kgp.vg
vg autoindex -p 1mb1kgp -w giraffe -P "VG w/ Variant Paths:1mb1kgp.vg" -P "Giraffe Distance Index:1mb1kgp.dist" -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz
vg giraffe -Z 1mb1kgp.giraffe.gbz -f reads/1mb1kgp_longread.fq >longread.gam -U 300 --progress --track-provenance --align-from-chains
# This is an 8001 bp read with 1 insert and 1 substitution
is "$(vg view -aj longread.gam | jq -r '.score')" "7989" "A long read can be correctly aligned"
is "$(vg view -aj longread.gam | jq -r '.score')" "7999" "A long read can be correctly aligned"
is "$(vg view -aj longread.gam | jq -c '.path.mapping[].edit[] | select(.sequence)' | wc -l)" "2" "A long read has the correct edits found"
is "$(vg view -aj longread.gam | jq -c '. | select(.annotation["filter_3_cluster-coverage_cluster_passed_size_total"] <= 300)' | wc -l)" "1" "Long read minimizer set is correctly restricted"

Expand Down

1 comment on commit 5dc1f7d

@adamnovak
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

vg CI tests complete for branch wfa-full-length-bonus. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 17324 seconds

Please sign in to comment.