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Fix/export tests #103

Merged
merged 5 commits into from
Jan 13, 2025
Merged

Fix/export tests #103

merged 5 commits into from
Jan 13, 2025

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mmolari
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@mmolari mmolari commented Jan 3, 2025

I corrected and extended tests for core-genome alignment export and gfa export.

concerning the core-genome alignment export:

  • I use a vector of blocks instead of a Btree for the blocks on the guide strain. If I understand correctly when iterating over the latter one gets blocks in the order of the key (the block id) while we want to maintain the order of the guide strain.
  • I extended the test with a more complete example, that involves different orders for different guide strains and different strandedness of different blocks

concerning the gfa export:

  • I removed the implementation of Edge and use the one already present in circularize, that is invariant under edge inversion. In this way edges traversed in different directions are still reported only once.
  • I added a more complete test example.

I also tried to open the produced gfa files with bandage, and everything seems in order:

image

@mmolari mmolari mentioned this pull request Jan 8, 2025
@ivan-aksamentov ivan-aksamentov merged commit 07d89dc into rust Jan 13, 2025
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@ivan-aksamentov ivan-aksamentov deleted the fix/export-tests branch January 13, 2025 10:57
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2 participants