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Make the default surjection max_anchors unlimited #4338

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merged 2 commits into from
Jul 19, 2024
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Changelog Entry

To be copied to the draft changelog by merger:

  • vg surject now uses an unlimited --max-anchors by default

Description

This should fix #4336 and make the defaults make more sense for long reads.

@adamnovak adamnovak force-pushed the unlimited-anchors branch from c50ecd4 to 15c38d7 Compare July 15, 2024 19:04
@adamnovak
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@jeizenga When you were looking at lifting the anchor limit and changed the default in the header, were you testing with Giraffe-integrated surjection and not vg surject? Since it looks like this PR still changes the default in vg surject itself.

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Honestly, I didn't really plan to test these changes, but I think it makes sense to raise the limit in both.

@adamnovak adamnovak merged commit 95fd1da into master Jul 19, 2024
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Turn off surjection anchor limit by default
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