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skoren

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Commits on Jan 26, 2021

• Fix out of bounds issue marbl#1878

  skoren

  committed
  e90f476

Commits on Dec 11, 2020

• Check for out of bounds while adjusting band, not just the first time (fix marbl#1845)

  skoren

  committed
  af771ef

Commits on Nov 13, 2020

• Update tag

  skoren

  committed
  76b1263

• Fix crash with tiny alignments and fix incorrect check for circularization

  skoren

  committed
  4b8448f

• Add functions to get non-contained first/last read and standardize their usage

  skoren

  committed
  ab08d0c

• Switch to non-vectorized version

  skoren

  committed
  a58af29

Commits on Oct 19, 2020

• Update faq.rst

  skoren

  authored
  2caad53

Commits on Sep 5, 2020

• Relax template alignment positions to account for optimize positions

  skoren

  committed
  2c12c35

• Allow last alignment to be parallel

  skoren

  committed
  c1329f7

Commits on Sep 2, 2020

• Update tutorial.rst

  skoren

  authored
  2a31172

• Update quick-start.rst

  skoren

  authored
  b8be124

• update to new read options, remove unitigs

  skoren

  authored
  556a7d7

• Update faq.rst

  skoren

  authored
  1ba2493

Commits on Aug 25, 2020

• Fix bogus position computation, don't use optimize positions

  skoren

  committed
  d4d3779

Commits on Aug 23, 2020

• Update logging with more details

  skoren

  committed
  139f30a

• Update positions after building the template and stop using scaling factor, make banding and error rate parameters defined in one place

  skoren

  committed
  be3b105

Commits on Aug 12, 2020

• Leave sort in, some users of this function (e.g. correction) don't provide sorted inputs

  Show description for 601e2fd
  skoren

  committed
  601e2fd

Commits on Aug 11, 2020

• Remove initial sort, input should be sorted already, add assert instead to make sure that is the case

  skoren

  committed
  06c84a9

• Don't use only best edges to circularize

  skoren

  committed
  c6ef4f7

• Add last sort to make sure positions are correct after stashing

  skoren

  committed
  d8d16e5

• Actually stash/save the correct read

  skoren

  committed
  9ff1612

Commits on Jul 22, 2020

• Start with more restrictive sizes on the expected overlap. Don't change error rate and size of overlap at the same time, try all sizes at one error rate, then increase error rate and try again, and…

  Show description for d3aa1b3
  skoren

  committed
  d3aa1b3

Commits on Jul 8, 2020

• Limit error rate to maximum specified when incrementing

  skoren

  committed
  81462be

• Cleanup parameters for hifi, standardize the ca/cp parameters across datasets

  skoren

  committed
  3507781

• Try more conservative alignments when building layout first, then expand size and error rate allowed

  skoren

  committed
  f3947bf

Commits on Jul 7, 2020

• Merge before checking for confusion, fix logging message

  skoren

  committed
  0fe9e38

Commits on Jun 29, 2020

• Disable overly verbose logging unless requested

  skoren

  committed
  68b9706

Commits on May 29, 2020

• Actually use the overlap parameter and change default to be consistent with what we had hardcoded

  skoren

  committed
  14fca27

Commits on May 28, 2020

• Add a very quick read randomization to deal with reads used multiple times in input layouts, clean up some code duplication a bit

  skoren

  committed
  1400b39

Commits on May 27, 2020

• Remove complex repeat bubble rule and replace with simplified cycle check instead

  skoren

  committed
  9fb4214

• tiny bit of dead cone cleanup + fix print

  skoren

  committed
  a05b7ba

• auto increase bogart error rate up to allowed maximum or mean when we notice thresholds are too restrictive

  skoren

  committed
  a334137

• Update default bubble identity and deviation

  skoren

  committed
  39bd894

• set pacbio parameters for hifi data too

  skoren

  committed
  6949a83

Commits on May 21, 2020

• Update faq.rst

  skoren

  authored
  cafc287

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