add_seq_context         Add flanking sequence context to a VCF data
                        frame
add_transcript_strand   Annotate a VCF data frame with transcript
                        strand information
all.abundance           K-mer abundances for density calculations
annot_vcf_to_476_catalog
                        Convert an annotated indel VCF to a Koh
                        476-category catalog
annot_vcf_to_83_catalog
                        Convert an annotated indel VCF to a COSMIC
                        83-category catalog
annot_vcf_to_89_catalog
                        Convert an annotated indel VCF to a Koh
                        89-category catalog
annotate_id_vcf         Annotate an in-memory ID (indel) VCF with
                        sequence context, transcript strand, and COSMIC
                        / Koh indel categories
annotate_sbs_or_dbs_vcf
                        Annotate an SBS or DBS VCF with flanking
                        sequence context and transcript strand
as_catalog              Turn a numeric matrix into a
                        mutational-spectrum catalog
catalog_attrs           Report the attributes of an mSigSpectra catalog
catalog_row_order       Return catalog row orders for all supported
                        catalog types
categorize_1_justified_indel
                        Given a indel and its sequence context,
                        categorize it
cbind_catalogs          Combine catalogs across samples (column-bind)
change_476_type_ids_to_open_intervals
                        Change 476-type indel category identifiers to
                        use right-open repeat intervals
change_89_type_ids_to_open_intervals
                        Change 89-type indel category identifiers to
                        use right-open repeat intervals
check_and_remove_discarded_variants
                        Check a VCF for common variant-level problems
                        and remove the offenders
collapse_catalog        Collapse a higher-resolution catalog to a
                        lower-resolution one
infer_trans_ranges      Infer transcript ranges for a reference genome
is_catalog              Check whether an object looks like an
                        mSigSpectra catalog
justify_id_vcf          Add sequence context and transcript information
                        to an in-memory ID (insertion/deletion) VCF,
                        and confirm that they match the given reference
                        genome
justify_indel           Move the notional position of a deletion or
                        insertion as far left as possible.
read_catalog            Read a mutational-spectrum catalog from a file
read_vcf                Read a VCF file into a data.table,
                        caller-agnostically
read_vcfs               Read multiple VCF files
seg_simple              Segment a single indel sequence using Rcpp
                        interface
segment_simple_cpp      Segment a single indel using Rcpp interface
split_vcf               Split a mixed-mutation VCF into SBS / DBS / ID
                        sub-tables
subset_catalog          Subset a catalog while preserving attributes
trans.ranges            Transcript ranges for transcriptional strand
                        annotation
transform_catalog       Transform a catalog between counts and density
vcf_to_dbs_catalog      Build a DBS mutational-spectrum catalog from an
                        annotated DBS VCF
vcf_to_id_catalog       Build an ID (indel) mutational-spectrum catalog
                        from an annotated ID VCF
vcf_to_sbs_catalog      Build an SBS mutational-spectrum catalog from
                        an annotated SBS VCF
write_catalog           Write a mutational-spectrum catalog to a file
