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Compute outside-to-outside TLENs properly #4516

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merged 3 commits into from
Feb 3, 2025
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@adamnovak adamnovak commented Jan 31, 2025

Changelog Entry

To be copied to the draft changelog by merger:

  • TLEN for read 1 starting inside read 2 will no longer be shorter than the union of the reads in vg surject.
  • TLEN computation handles more CIGAR operations in case we decide to use them.

Description

Even if the reads overlap we need an outside-to-outside TLEN like the function claims to calculate.

This adds a bunch of unit tests for TLEN computation edge cases based on the SAM spec, and makes us pass them.

Even if the reads overlap we need an outside-to-outside TLEN like the function claims to calculate.
@adamnovak adamnovak merged commit 1180ebf into master Feb 3, 2025
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