analyze_fragmentation   Provides fragment ends analysis
bin_fragment_size       Gets histogram of fragment lengths from a bam
                        file
create_background_panel
                        Creates a background panel from a list of bam
                        files
create_black_list       Creates a black list of genomic loci based on a
                        background panel created from a list of bam
                        files (e.g. healthy samples)
extract_trinucleotide_context
                        Extracts the trinucleotide context for a set of
                        mutations
filter_mutations        Filters a set of mutations
get_background_rate     Computes the background mismatch rate from a
                        bam file
get_fragment_size       Gets fragment lengths from a bam file
get_mutations_fragment_size
                        Gets reads fragment lengths for a list of
                        mutations
get_mutations_read_counts
                        Counts ref and alt reads for a set of mutations
get_mutations_read_names
                        Gets names of the reads showing reference and
                        alternative allele of a list of mutations
merge_mutations_in_phase
                        Collapses mutations in phase into one event
mutations               Example mutations data to use with ctDNAtools
                        package
summarize_fragment_size
                        Summarizes fragment size in defined genomic
                        regions
targets                 Example Genomic targets to use with ctDNAtools
                        package
test_ctDNA              Tests the ctDNA positivity of a sample
vcf_to_mutations_df     Helper function to read a vcf into the required
                        format of mutations data frame
