v0.5.0

0.5.0 (2025-01-24)

Continuous Integration

• pre-commit reformatting (4834ee0)

Miscellaneous Chores

• fix version (6967db9)
• version bump (58cdd6d)

Documentation

• update README (08458a6)

Features

• detect AMR-determining SNPs in promoters if specified (582ea7a)
• estimate cellular copy numbers by calculating coverage across the longest read for each AMR gene, then normalise by mean read depth across core genes (68566de)
• genotype novel SNPs in promoters (ba8e654)

Bug Fixes

• check for float (0eef5b2)
• detect presence of causative SNPs without full allele matches] (7512592)
• estimate mean depth only from core genes (49006e4)
• fastq file path fix (52a6fbb)
• fix adding promoter results to existing df (2a55d4f)
• fix adding rpomoter results to existing df (8fa1c92)
• only add promoters to results if non ref (6afa85b)
• only add promoters to results if non ref (1c30eec)
• remove depreciate append to df (b0f63e9)
• remove underscores in read names and remove redundany graph outputs (c28172c)
• tweak mpileup params (f23bfa2)
• update graph_operations (921953b)
• use min coverage of node in path to estimate copy number (d5c1291)
• use samtools mpileup to estimate cellular copy number to include secondary alignments (440096e)

Styles

• flake8 formatting (cde598d)

Tests

• add test files (d698e0a)