useDynLib(cigarillo)

import(methods)
importFrom(stats, setNames)

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(Biostrings)

export(
    ## cigar_ops_visibility.R:
    CIGAR_OPS,
    cigar_ops_visibility,

    ## explode_cigars.R:
    validate_cigars,
    explode_cigar_ops, explode_cigar_oplens,
    cigars_as_RleList,

    ## tabulate_cigar_ops.R:
    tabulate_cigar_ops,

    ## cigar_extent.R:
    cigar_extent_along_ref,
    cigar_extent_along_query,
    cigar_extent_along_pwa,

    ## trim_cigars.R:
    trim_cigars_along_ref,
    trim_cigars_along_query,
    narrow_cigars_along_ref,
    narrow_cigars_along_query,

    ## cigars_as_ranges.R:
    cigars_as_ranges_along_ref,
    cigars_as_ranges_along_query,
    cigars_as_ranges_along_pwa,

    ## project_positions.R:
    query_pos_as_ref_pos,
    ref_pos_as_query_pos,

    ## project_sequences.R:
    project_sequences,

    ## map_ref_ranges_to_query.R:
    map_ref_ranges_to_query,
    fast_map_ref_ranges_to_query
)

