CHANGELOG.rst

Changelog

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

The format is based on Keep a Changelog.

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