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Don't duplicate source GBZ in autoindex #4503

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merged 2 commits into from
Jan 24, 2025
Merged

Don't duplicate source GBZ in autoindex #4503

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007adba
Don't duplicate source GBZ in autoindex
adamnovak Jan 23, 2025
f2151ac
Log potentially wrong error message
adamnovak Jan 23, 2025
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3 changes: 3 additions & 0 deletions src/subcommand/autoindex_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -352,6 +352,9 @@ int main_autoindex(int argc, char** argv) {
}
if (!gbz_name.empty()) {
registry.provide("GBZ", gbz_name);
// Also mark this as the Giraffe GBZ so if we index for Giraffe we won't duplicate it.
// TODO: Why are these separate?
registry.provide("Giraffe GBZ", gbz_name);
}


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1 change: 1 addition & 0 deletions test/t/15_vg_surject.t
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Expand Up @@ -202,6 +202,7 @@ is "${?}" "1" "Surjection fails when using the wrong graph for GAM"
is "$(cat err.txt | grep 'cannot be interpreted' | wc -l)" "1" "Surjection of GAM to the wrong graph reports the problem"
vg surject -x tiny.vg -s -t 1 -m mapped.gamp >/dev/null 2>err.txt
is "${?}" "1" "Surjection fails when using the wrong graph for GAMP"
cat err.txt 1>&2
is "$(cat err.txt | grep 'cannot be interpreted' | wc -l)" "1" "Surjection of GAMP to the wrong graph reports the problem"

rm x.vg x.pathdup.vg x.xg x.gcsa x.gcsa.lcp x.gam mapped.gam mapped.gamp tiny.vg err.txt
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