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Commits on Dec 9, 2022

• Bump version 1.4.1

  aresti

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  04837c1

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• Fix language version in pyproject.toml

  aresti

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  6fc4e87

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• Update README

  aresti

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  c6311d4

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• Fix failing test for no such option

  aresti

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Commits on Dec 2, 2022

• CI python versions should be strings

  aresti

  committed
  838a82d

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• Drop support for python 3.6

  aresti

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  04a3225

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• Upgrade click, fixes incompatibility with latest version of Black for CI

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  committed
  1f7bb5c

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Commits on Dec 1, 2022

• Bump version 1.4.0

  aresti

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  52f89ad

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• Update pre-commit conf

  aresti

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  86f75b7

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Commits on Jun 5, 2021

• Fix bug where left/right primers are not checked against one another for interactions (same region)

  aresti

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Commits on May 20, 2021

• Remove test against primer3 base penalty since we have diverged

  aresti

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• Add primer seq as addition col in bed file

  aresti

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  0742922

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• Added config.PRIMER_MAX_BASE_PENALTY, tuned penalty weighting, improved debug log

  aresti

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Commits on May 19, 2021

• Drop standalone homodimer check; use same method as for heterodimers

  aresti

  committed
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Commits on May 18, 2021

• Fix boolean logic for heterodimer & homodimer check

  aresti

  committed
  cac3a9e

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• Don't store thermo objs as primer candidate attributes; fixes pickle debug output

  aresti

  committed
  f6e51d4

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• Standardise use of primer3 wrapper functions

  aresti

  committed
  0656b89

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• only run homodimer check against top candidates (improve speed); replace stray constants with config

  aresti

  committed
  d73f10c

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Commits on May 17, 2021

• Merge pull request #28 from joshquick/master

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  aresti

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• Refactor failed alignment & revert indel handling

  aresti

  committed
  6a5e272

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• Appease linter

  

  Josh Quick

  committed
  0e11076

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Commits on May 13, 2021

• Add homodimer to hard filter and use 3' exact matches (Itokawa et al., 2020) for heterodimer checks

  

  Josh Quick

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Commits on Apr 21, 2021

• Merge feat-improved-indel-handling

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  aresti

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  0a37e1e

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• Fix calc_max_homo bug where nothing returned in the case of two adjacent homopolymers of same length

  aresti

  committed
  f1a8358

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• Fix failing tests

  aresti

  committed
  8eb1a19

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• Fix pre-commit-config, pin to version of black

  aresti

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  f5c06c8

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Commits on Feb 2, 2021

• allow up to 200 refs

  aresti

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  c4d5d47

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Commits on Jul 29, 2020

• Allow indels in alignments; score as mismatches

  aresti

  committed
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Commits on Jul 28, 2020

• Remove stray space in format string

  aresti

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  2b52e34

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• Tidy Region class, combine with Window and remove needless inheritance.

  aresti

  committed
  696d86b

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• Tidy up conftest fixture docstrings

  aresti

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• Iterate on Direction enum rather than left/right statements to call Region._log_debug

  aresti

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  7d5e209

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• Rationalise Region._sort_candidates to use instance

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  03805a9

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• Move changelog references to end of file

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  bb0b806

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• Bump version 1.3.2

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