TrueConsense v0.5.1

Bug Fixes

• change the seq_id in the output gff to match the input samplename (37b7d9e)

TrueConsense v0.5.0

⚠ BREAKING CHANGES

• Use output files in stead of folders

Features

• Use output files in stead of folders (b0dfef8)

Documentation

• Update docs for file output in stead of folders (7c47393)

TrueConsense v0.4.0

⚠ BREAKING CHANGES

• Use only a single minimum coverage level

Features

• Use only a single minimum coverage level (cdd29b7)

Bug Fixes

• Fix WriteOutputs number of args (8bf72f8)

Performance Improvements

• Use pysam directly in stead of pysamstats (afd8c0a)

Dependencies

• remove parmap as a dependency (0aaed4d)

Documentation

• add docstring to TrueConsense.Outputs (4855ee9)
• add docstrings to functions in TrueConsense.Ambig (4e8a138)
• add docstrings to functions in TrueConsense.Coverage (47d8c89)
• add docstrings to functions in TrueConsense.Events (6d754e3)
• add docstrings to functions in TrueConsense.indexing (650a5d1)
• add docstrings to functions in TrueConsense.Sequences (5abdb81)
• add docstrings to functions of TrueConsense.ORFs (b52a750)
• update readme and docs-index to support a single coverage level (f9fd73e)
• update TrueConsense docs to only feature a single coverage level (53cecc3)

TrueConsense v0.3.0

Features

• add arg to override index with pre-made index on certain positions (9b3227c)

Documentation

• add changelog page (2f29130)
• add explanation of --index-override flag to docs (ac4ac4b)

First release: TrueConsense v0.2.0

Initial versioned release of TrueConsense with version 0.2.0

TrueConsense is a nucleotide consensus caller capable of creating a biologically valid consensus-sequence in reference-based virus sequencing experiments.
TrueConsense compensates for common sequencing and/or alignment artefacts, keeps track of open reading frames, and is able to generate consensus-sequences on multiple coverage-thresholds at the same time.