From 007adba4893d1a1eddd485c9e469de7528c9f91f Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Thu, 23 Jan 2025 13:01:57 -0500 Subject: [PATCH 1/2] Don't duplicate source GBZ in autoindex --- src/subcommand/autoindex_main.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/subcommand/autoindex_main.cpp b/src/subcommand/autoindex_main.cpp index ab72408d31..962f650a77 100644 --- a/src/subcommand/autoindex_main.cpp +++ b/src/subcommand/autoindex_main.cpp @@ -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); } From f2151ac8c2b5077f5367bd8fe2ace88d503e65f9 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Thu, 23 Jan 2025 14:30:42 -0500 Subject: [PATCH 2/2] Log potentially wrong error message --- test/t/15_vg_surject.t | 1 + 1 file changed, 1 insertion(+) diff --git a/test/t/15_vg_surject.t b/test/t/15_vg_surject.t index 28d8992c09..2f852beb0b 100644 --- a/test/t/15_vg_surject.t +++ b/test/t/15_vg_surject.t @@ -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