_rustybam() {
    local i cur prev opts cmds
    COMPREPLY=()
    cur="${COMP_WORDS[COMP_CWORD]}"
    prev="${COMP_WORDS[COMP_CWORD-1]}"
    cmd=""
    opts=""

    for i in ${COMP_WORDS[@]}
    do
        case "${i}" in
            rustybam)
                cmd="rustybam"
                ;;
            
            help)
                cmd+="__help"
                ;;
            liftover)
                cmd+="__liftover"
                ;;
            nucfreq)
                cmd+="__nucfreq"
                ;;
            repeat)
                cmd+="__repeat"
                ;;
            stats)
                cmd+="__stats"
                ;;
            suns)
                cmd+="__suns"
                ;;
            *)
                ;;
        esac
    done

    case "${cmd}" in
        rustybam)
            opts=" -t -h -V  --threads --help --version  stats nucfreq suns repeat liftover help"
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 1 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        
        rustybam__help)
            opts=" -h -V  --help --version  "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        rustybam__liftover)
            opts=" -b -q -l -t -h -V  --bed --qbed --largest --threads --help --version  <paf> "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --bed)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -b)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        rustybam__nucfreq)
            opts=" -r -b -s -t -h -V  --region --bed --small --threads --help --version  <BAM> "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --region)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -r)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --bed)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -b)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        rustybam__repeat)
            opts=" -m -t -h -V  --min --threads --help --version  <fasta> "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --min)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -m)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        rustybam__stats)
            opts=" -q -p -t -h -V  --qbed --paf --threads --help --version  <BAM> "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
        rustybam__suns)
            opts=" -k -m -v -t -h -V  --kmersize --maxsize --validate --threads --help --version  <fasta> "
            if [[ ${cur} == -* || ${COMP_CWORD} -eq 2 ]] ; then
                COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
                return 0
            fi
            case "${prev}" in
                
                --kmersize)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -k)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --maxsize)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -m)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                --threads)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                    -t)
                    COMPREPLY=($(compgen -f "${cur}"))
                    return 0
                    ;;
                *)
                    COMPREPLY=()
                    ;;
            esac
            COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
            return 0
            ;;
    esac
}

complete -F _rustybam -o bashdefault -o default rustybam