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Add a test for surjection orientation independence
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@adamnovak
adamnovak committed Oct 21, 2024
1 parent 09d2e7e commit 1ff1009
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2 changes: 2 additions & 0 deletions test/surject/opposite_strands.gaf
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forward 35 0 35 + >56629809>56629810>56629811>56629814>56629815>56629819>56629820>56629822 132 97 132 35 35 0 cs:Z::35
reverse 35 0 35 + <56629822<56629820<56629819<56629815<56629814<56629811<56629810<56629809 132 0 35 35 35 0 cs:Z::35
43 changes: 43 additions & 0 deletions test/surject/opposite_strands.gfa
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H VN:Z:1.1 RS:Z:GRCh38 CHM13
S 56629807 G
S 56629808 T
S 56629809 TTTCTGATTATAAATATTGCACATGTATTGATTACATAAATCCATATACTATAAAACTGATATTTAAGAGAATAAAAGTCCCAACCTCAGAATTAACTACTG
S 56629810 C
S 56629811 A
S 56629812 A
S 56629813 C
S 56629814 CCCCC
S 56629815 C
S 56629816 G
S 56629817 T
S 56629818 T
S 56629819 T
S 56629820 TTTTTTTTTTT
S 56629821 T
S 56629822 GATGGAGTCT
S 56629823 C
S 56629824 G
W CHM13 0 chr8 81560724 81560860 >56629807>56629809>56629810>56629813>56629814>56629817>56629818>56629819>56629820>56629821>56629822>56629824
W GRCh38 0 chr8 35183939 35184073 >56629807>56629809>56629810>56629811>56629814>56629815>56629819>56629820>56629822>56629823
L 56629807 + 56629809 + 0M
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4 changes: 3 additions & 1 deletion 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 47
plan tests 48

vg construct -r small/x.fa >j.vg
vg index -x j.xg j.vg
Expand Down Expand Up @@ -198,3 +198,5 @@ is "$(vg surject -x x.xg -M -m -s -i -t 1 mapped.gamp | grep -v '@' | wc -l)" 80

rm x.vg x.pathdup.vg x.xg x.gcsa x.gcsa.lcp x.gam mapped.gam mapped.gamp

is "$(vg surject -p CHM13#0#chr8 -x surject/opposite_strands.gfa --prune-low-cplx --sam-output --gaf-input surject/opposite_strands.gaf | grep -v "^@" | cut -f3-12 | sort | uniq | wc -l)" "1" "vg surject low compelxity pruning gets the same alignment regardless of read orientation"

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vg CI tests complete for branch lr-giraffe. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 17453 seconds

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