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avoid duplicates in `query_transitive` #26

Merged

AndreaGuarracino merged 1 commit into main from remove_dup_query_transitive

Oct 9, 2024

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AndreaGuarracino commented Oct 9, 2024

query_transitive can return (lots of) duplicated entries:

impg -p x.paf -r SGDref#1#chrXVI:20000-30000 -x           
SGDref#1#chrXVI 20000   30000   .       +
SK1#1#chrXVI    22204   32216   .       +
SGDref#1#chrXVI 20000   30000   .       +
S288C#1#chrXVI  20246   30246   .       +
SK1#1#chrXVI    22204   32216   .       +
SK1#1#chrXVI    22204   32216   .       +

We now avoid them by leveraging the HashSet we are already using to avoid querying the same intervals during the transitive closures:

impg -p x.paf -r SGDref#1#chrXVI:20000-30000 -x             
SGDref#1#chrXVI 20000   30000   .       +
SK1#1#chrXVI    22204   32216   .       +
S288C#1#chrXVI  20246   30246   .       +


          avoid duplicates in query_transitive

9a83d37

AndreaGuarracino merged commit 8bb2712 into main

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AndreaGuarracino mentioned this pull request

Pangenome partitioning #29

Merged

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