# ----------------------------------------------------------------------------
# Copyright (c) 2025, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

from .bracken import estimate_bracken
from .database import build_kraken_db
from .classification import classify_kraken2, _classify_kraken2
from .select import (
    kraken2_to_features,
    kraken2_to_mag_features,
)
from .merge import _merge_kraken2_results
from .filter import (
    _filter_kraken2_results_by_metadata,
    _filter_kraken2_reports_by_abundance,
    _align_outputs_with_reports,
    filter_kraken2_results,
)
from .collapse import (
    collapse_contigs,
    map_taxonomy_to_contigs,
    _visualize_collapsed_contigs,
)

__all__ = [
    "build_kraken_db",
    "classify_kraken2",
    "_classify_kraken2",
    "estimate_bracken",
    "kraken2_to_features",
    "kraken2_to_mag_features",
    "collapse_contigs",
    "map_taxonomy_to_contigs",
    "_visualize_collapsed_contigs",
    "_filter_kraken2_reports_by_abundance",
    "_filter_kraken2_results_by_metadata",
    "_align_outputs_with_reports",
    "filter_kraken2_results",
    "_merge_kraken2_results",
]
