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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

0.8.0

Fixed

  • The computation of the empirical accuracy by alignparse.consensus.empirical_accuracy is now done by computing the relevant quantitites in log space which makes it more robust to large numbers. Thanks to @fc-jian for inspiring this via [this issue](#106).

0.7.1

Fixed

  • Fix bug in allow_arbitrary_numbers to MutationRenumber when the arbitrary str are the old rather than new numbers.

0.7.0

Added

  • Added allow_arbitrary_numbers to MutationRenumber to allow arbitrary strings as site numbers.

0.6.3

Fixed

  • Fix bug in handling minimap2 errors ([see this issue](#99))
  • Pass formatting with new black version
  • Pass tests with new pandas version.
  • Fixed simple_mut_consensus for newer versions of pandas when goruping by just one variable.

Changed

  • Change code linting to ruff rather than flake8.
  • Test with GitHub Actions rather than Travis CI.
  • Remove mybinder examples.
  • Test on Python 3.11 rather than 3.9.
  • Don't allow pysam version 0.22.1 as it was causing some type of OPENSSL import error.
  • Test with minimap2 version 2.22

0.6.2

Fixed

  • Require python 3.8 or greater.

0.6.1

Fixed

  • Pass tests on newer dependency versions, test on python 3.9.

0.6.0

Added

  • Can parse reports from pbccs version 6.0.

0.5.0

Added

  • MutationRenumber accepts parameter allow_letter_suffixed_numbers to allow sites with lowercase letter suffixes (e.g, 214a)

0.4.1

Fixed

  • Remove deprecated pandas.DataFrame.append

0.4.0

Added

  • MutationRenumber accepts gap (-) and stop codo (*) characters.
  • Started requring black formatting

0.3.0

Added

  • InFrameDeletionsToSubs class.
  • simple_mutconsensus takes None as parameter for max_sub_diffs and max_indel_diffs
  • simple_mutconsensus takes arguments min_support and max_minor_greater_or_equal

0.2.6

Fixed

  • Fixed bug in add_mut_info_cols when index is not unique.

0.2.5

Added

  • merge_dels function that merges consecutive deletion strings.

0.2.4

Fixed

  • consensus.simple_mutconsensus works with just one grouping column.

0.2.3

Fixed

  • consensus module handles negative site numbers.

0.2.2

Fixed

  • sort_mutations and MutationRenumber handle negative site numbers.

0.2.1

Added

  • sort_mutations function to sort mutations by site, and optionally concatenate them.

0.2.0

Added

  • MutationRenumber class to enable re-numbering of mutations.

0.1.6

Fixed

  • Removed --for-only from OPTIONS_VIRUS_W_DEL

0.1.5

Added

  • Summaries now parses np (number of passes) tags from ccs version 5.0 FASTQs.

0.1.4

Added

  • Summaries now handles summaries from ccs version 5.0

0.1.3

Added

  • Added hspace as option to Targets.plot.

0.1.2

Added

  • Added select_target_names option to Targets.

0.1.1

Fixed

  • Fixed DataFrame querying bug in ./alignparse/ccs.py

0.1.0

Initial release