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Commits on Jan 11, 2023

• Make minkmer parameter non-positional

  skoren

  committed
  4b563b5

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• Enable use of minimum kmer count to filter matches

  skoren

  committed
  2c5dd8c

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Commits on Dec 16, 2022

• use minimum overlap not fixed 500bp (issue marbl#2181)

  skoren

  authored
  f29343c

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Commits on Oct 22, 2022

• Fix crash on empty links in align gfa

  skoren

  committed
  6eca3b1

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Commits on Oct 19, 2022

• Update quick-start.rst

  skoren

  authored
  790082e

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Commits on Jul 29, 2022

• Additional parallelization

  skoren

  committed
  48786ab

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• Minor update to try contained reads only at the end

  skoren

  committed
  584e01e

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Commits on May 24, 2022

• Fix inverted condition from last commit, doh!

  skoren

  committed
  09862fa

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Commits on May 17, 2022

• Updates to parameters, default to saving failed links

  skoren

  committed
  b438c06

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Commits on May 16, 2022

• Fix infinite loop when backtracking

  skoren

  committed
  378fcde

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Commits on May 13, 2022

• Fix backtracking ignoring some candidates, allow contained reads to be used in last chance of backtracking

  skoren

  committed
  1982d12

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Commits on Apr 23, 2022

• Update consensus to use max error rate and regular error rate and specify which reads are allowed to use higher error rate

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  skoren

  committed
  15f3418

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Commits on Apr 14, 2022

• update for clang build

  skoren

  committed
  cb3321c

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Commits on Apr 6, 2022

• Another round of code cleanup, first version that runs to the end on a large genome

  skoren

  committed
  1efc76e

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• Fix over-trimming of short contig

  skoren

  committed
  1a710da

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Commits on Mar 18, 2022

• Fix bug that would fail to reset error rate after a gap on the last read

  skoren

  committed
  ce56a1e

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Commits on Mar 10, 2022

• Remove limit of AS_MAX_READLEN on utgcns

  skoren

  committed
  7041856

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• Fixes to how pre-consensus sequences are aligned to post-consensus ones. Fixes in link cigar re-calculation, still a work in progress

  skoren

  committed
  001fa55

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Commits on Feb 18, 2022

• A few updates to handle larger extensions of original sequence and handle gfa sequences which have no consensus

  skoren

  committed
  5cec8b0

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Commits on Feb 17, 2022

• Update alignGFA to work with verkko outputs

  skoren

  committed
  3b4a21b

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Commits on Jan 15, 2022

• Terminate package format string to avoid overflow

  skoren

  committed
  a339473

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Commits on Dec 28, 2021

• Fix bug when original length is negative

  skoren

  committed
  2306043

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Commits on Dec 21, 2021

• Fix check for hash table overflow

  skoren

  committed
  af0f896

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Commits on Dec 20, 2021

• Fix underflow of overlap length (<0)

  skoren

  committed
  140dc72

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• Skip contigs not in range requested by the user

  skoren

  committed
  fe6d364

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• Add some extra space to the hash table to avoid cases where we are unable to load the last few reads

  skoren

  committed
  dd10d72

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Commits on Dec 17, 2021

• Allow one read's worth of slush when loading data into hash

  skoren

  committed
  165ff44

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• Remove warning

  skoren

  committed
  fb436f4

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Commits on Dec 10, 2021

• Another bugfix, reset candidate ID after trimming template

  skoren

  committed
  6d46939

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Commits on Dec 3, 2021

• Avoid negative values comparing to uint32

  skoren

  committed
  b281489

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Commits on Dec 2, 2021

• Remove attempts to increase/decrease overlap, not needed with more accurate positions for reads and just likely to introduce a bad alignment

  skoren

  committed
  b28b506

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Commits on Dec 1, 2021

• Another fix to handle trimming back better

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  committed
  ed69934

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Commits on Nov 30, 2021

• When alignments fail, try other candidates in the list we had skipped. If all those fail, trim back the template to see if we can find an alignment then. More robust to bad/chimeric read ends.

  skoren

  committed
  61edd0e

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• Remove spaces at end of lines

  skoren

  committed
  b1c93ad

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• Fix overlap increase/decrease to avoid out of bounds errors

  skoren

  committed
  ff35285

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