Release v2.6.0 #144
Merged
Release v2.6.0 #144
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…undant and adds large amounts of data to batch samples
…undant and adds large amounts of data to batch samples
… being filtered for failed kmers
- added --min-kmer-frac for exclusion of low abundance kmers from subtype calling - detailed report adds columns: `kmer_fraction`, `total_refposition_kmer_frequency`, `is_kmer_fraction_okay` - increased default --max-kmer-freq for amplicon seq data compatibility
Add bump2version config for easy version updating
- refactoring and reformatting; fixed some docstrings; simplified some logic - moved some functions to more appropriate places - replaced string.format with f-string literals - moved 'check_total_kmers' call to right after parsing of CLI args - replaced bio_hansel.parsers._parse_fasta with BioPython's Bio.SeqIO.FastaIO.SimpleFastaParser; forcing uppercase of sequence - cleaned up some tests - updated help message to show program name and version as well as nice list of built-in schemes - ignoring/fixed some warnings when pytest Signed-off-by: Peter Kruczkiewicz <peter.kruczkiewicz@gmail.com>
Release v2.6.0
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changes
--min-kmer-fracfor exclusion of low abundance kmers from subtype callingkmer_fraction,total_refposition_kmer_frequency,is_kmer_fraction_okay--max-kmer-freqfor amplicon seq data compatibility$ bump2version major|minor|patchstring.formatwith f-string literalscheck_total_kmerscall to right after parsing of CLI argsbio_hansel.parsers._parse_fastawith BioPython'sBio.SeqIO.FastaIO.SimpleFastaParser; forcing uppercase of sequence