BarcodeMapper 1.1.0

The first tagged release. Version 1.0.0 was an untagged development snapshot; its changes are included here.

Added

• Snakemake workflow for database preparation, read filtering, Bowtie2 mapping, taxonomy assignment, aggregation, and HTML reporting.
• Local and Slurm profiles, mapping presets, and paired FASTQ input support.
• Package metadata, MIT license, software citation, release checks, and build CI.
• End-to-end synthetic workflow tests and a run manifest with tool versions, parameters, database and source checksums, and sample filtering counts.
• Documentation for installation, source provenance, limitations, validation, and release steps.
• Allow barcodemapper --build without source files to fetch the current BOLD and UNITE releases, record their provenance, and skip or repair an already current database.

Changed

• Map with Bowtie2's exhaustive alignment mode to preserve ambiguous taxonomic matches.
• Count edit distance against actual aligned bases and expose adapter, read-length, and complexity controls.
• Keep conflicting taxonomies for identical BOLD sequences so lowest-common-ancestor assignment can represent ambiguity.
• Make the HTML report self-contained and include zero-hit and kingdom-only assignments in its plots.
• Validate paired reads, numeric inputs, and database paths before starting Snakemake.
• Compress newly built reference FASTAs with gzip and read compressed databases directly for validation, indexing, and taxonomy overviews.

Fixed

• Use fastp's low-complexity flag with its threshold argument correctly.
• Preserve empty samples and unresolved taxonomy during aggregation and reporting.
• Pass paths safely to workflow commands and propagate Bowtie2 pipe failures.
• Generate missing analysis index and taxonomy overview files in the work directory instead of beside a shared reference FASTA.
• Handle sample names that match internal report column names.