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add integration test
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@jeizenga
jeizenga committed Dec 14, 2022
1 parent 9f6f93a commit 6bd831f
Showing 1 changed file with 11 additions and 5 deletions.
16 changes: 11 additions & 5 deletions test/t/52_vg_autoindex.t
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ BASH_TAP_ROOT=../deps/bash-tap

PATH=../bin:$PATH # for vg

plan tests 32
plan tests 34

rm auto.*

Expand Down Expand Up @@ -35,7 +35,7 @@ rm auto.*

# to add: GFA construction

vg autoindex -p auto -w mpmap -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf
vg autoindex -p auto -w mpmap -w rpvg -r tiny/tiny.fa -v tiny/tiny.vcf.gz -x tiny/tiny.gtf
is $(echo $?) 0 "autoindexing successfully completes indexing for vg mpmap with unchunked input"
is $(ls auto.* | wc -l) 6 "autoindexing creates 6 files for mpmap/rpvg"
vg sim -x auto.spliced.xg -n 20 -a -l 10 | vg mpmap -x auto.spliced.xg -g auto.spliced.gcsa -d auto.spliced.dist -B -t 1 -G - > /dev/null
Expand All @@ -45,18 +45,24 @@ is $(cat auto.txorigin.tsv | wc -l) 7 "transcript origin table has expected numb

rm auto.*

vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf
vg autoindex -p auto -w mpmap -r tiny/tiny.fa -x tiny/tiny.gtf
is $(echo $?) 0 "autoindexing successfully completes indexing for vg mpmap without variants"
is $(ls auto.* | wc -l) 4 "autoindexing creates 4 files for mpmap/rpvg without variants"

rm auto.*

vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/x.gtf -x small/y.gtf
is $(echo $?) 0 "autoindexing successfully completes indexing for vg mpmap with chunked input"
is $(ls auto.* | wc -l) 6 "autoindexing creates 6 files for mpmap/rpvg with chunked input"

rm auto.*

vg autoindex -p auto -w mpmap -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf
vg autoindex -p auto -w mpmap -w rpvg -r small/x.fa -r small/y.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf
is $(echo $?) 0 "autoindexing successfully completes indexing for vg mpmap with partially chunked input"

rm auto.*

vg autoindex -p auto -w mpmap -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf
vg autoindex -p auto -w mpmap -w rpvg -r small/xy.fa -v small/x.vcf.gz -v small/y.vcf.gz -x small/xy.gtf
is $(echo $?) 0 "autoindexing successfully completes indexing for vg mpmap with another partially chunked input"

rm auto.*
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1 comment on commit 6bd831f

@adamnovak
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vg CI tests complete for branch mpmap-softclip. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 10632 seconds

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