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Set snarl distance to 0 in path normalizer now that distance index is fixed. #4400

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merged 3 commits into from
Sep 26, 2024
Merged

Set snarl distance to 0 in path normalizer now that distance index is fixed. #4400

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59f3f24
fix typo in paths test
glennhickey Sep 17, 2024
c78dce7
set snarl distance to 0 in path normalize
glennhickey Sep 17, 2024
1a9fd57
Merge remote-tracking branch 'origin/master' into path-normalize
adamnovak Sep 23, 2024
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3 changes: 1 addition & 2 deletions src/traversal_clusters.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -384,8 +384,7 @@ void merge_equivalent_traversals_in_graph(MutablePathHandleGraph* graph, const u
SnarlDistanceIndex distance_index;
{
IntegratedSnarlFinder snarl_finder(*graph);
// todo: why can't I pass in 0 below -- I don't want any dinstances!
fill_in_distance_index(&distance_index, graph, &snarl_finder, 1);
fill_in_distance_index(&distance_index, graph, &snarl_finder, 0);
}

// only consider embedded paths that span snarl
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8 changes: 4 additions & 4 deletions test/t/11_vg_paths.t
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Expand Up @@ -90,10 +90,10 @@ diff original.fa norm_x4.fa
is $? 0 "path normalizer doesnt alter path sequences"

# note: x3 is x4 in reverse, so we key on that
grep x3 norm_x2.gfa | awk '{print $3}' > x4.path
grep x3 norm_x2.gfa | awk '{print $3}' >> x4.path
grep x3 norm_x2.gfa | awk '{print $3}'> x4.norm.path
grep x5 norm_x2.gfa | awk '{print $3}' >> x4.norm.path
grep x3 norm_x4.gfa | awk '{print $3}' > x4.path
grep x3 norm_x4.gfa | awk '{print $3}' >> x4.path
grep x3 norm_x4.gfa | awk '{print $3}'> x4.norm.path
grep x5 norm_x4.gfa | awk '{print $3}' >> x4.norm.path
diff x4.path x4.norm.path
is $? 0 "path normalizere correctly snapped all equivalent paths to x4"

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