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Commits on Nov 14, 2023

• Merge NAMs without using start of prev. hit

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• wip

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• Fix matches ending too early in PAF output

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  marcelm

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• Merge pull request #362 from ksahlin/samdiff-fix

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  marcelm

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• Update baseline commit

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Commits on Nov 13, 2023

• Let samdiff fail if no reads were in the input

  marcelm

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Commits on Oct 2, 2023

• Merge pull request #353 from ksahlin/dumpseeds

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  marcelm

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• Add dumpstrobes --seeds for writing out the full seed vector

  marcelm

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• Move count(_all)_randstrobes into anonymous namespace

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  marcelm

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• Merge pull request #351 from ksahlin/rl250

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• Merge pull request #350 from ksahlin/fix-accuracy

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  marcelm

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• Slightly improve accuracy for read length 250

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Commits on Sep 28, 2023

• Merge pull request #348 from ksahlin/tests

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  marcelm

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• Fix: Avoid nam id collisions that reduce accuracy

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  marcelm

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• Do not require strobealign to be in PATH when running tests

  marcelm

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• Merge pull request #347 from ksahlin/fixmem

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Commits on Sep 27, 2023

• Reduce memory usage when indexing

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Commits on Sep 26, 2023

• Merge pull request #345 from ksahlin/optimize-kslu

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  marcelm

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• Set optimized parameters for read lengths 50, 100, 125, 250, 300

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  marcelm

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• Add canonical read length 75 for lengths 66..90

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  marcelm

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• Merge pull request #346 from ksahlin/mini-xxh64

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Commits on Sep 21, 2023

• Replace xxh64 with a simplified version

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Commits on Sep 20, 2023

• Merge pull request #344 from ksahlin/readlenfix

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• Merge pull request #342 from ksahlin/randstrobe-hash

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Commits on Sep 19, 2023

• Fix read length estimation crash on chromosome-sized "reads"

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  marcelm

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• Factor out a randstrobe_hash function

  marcelm

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Commits on Sep 8, 2023

• Merge pull request #338 from ksahlin/wmin

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  marcelm

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• Allow w_min to be 0

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• Ensure that w_min <= w_max

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Commits on Sep 6, 2023

• Merge pull request #337 from ksahlin/refactor

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  marcelm

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• Let rescue_mate return an Alignment

  marcelm

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• Merge pull request #336 from ksahlin/nams

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  marcelm

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• Simplify

  marcelm

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• Remove an unnecessary call to reverse_nam_if_needed()

  marcelm

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• Simplify rescue_mate

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