Advanced Branch Mining Turtle (second/over)

--Variable Declarations
local mainShaftDim = "2x2"
local sideShaftDim = "2x1"
local shaftFreq = "3"
local totalCost = 0
local input = ""
local length = 0
local currentPos = 1
local chestDist = 0
local doFuel = false



--Function Declarations
-- Refuels the turtle with slots 1-15
function refuel()
    for i=1,15,1 do
        turtle.select(i)
        turtle.refuel(turtle.getItemCount(i))
    end
    turtle.select(1)
end

function dig()
    turtle.dig()
end

-- Mines the main 2x2 shaft of the system
function mainShaft()
    turtle.select(1)
    for i=1,4,1 do
        while turtle.detect() == true do
            dig()
        end
        turtle.forward()
        while turtle.detectUp() do
            turtle.digUp()
        end
        turtle.turnRight()
        while turtle.detect() == true do
            dig()
        end
        turtle.forward()
        while turtle.detectUp() do
            turtle.digUp()
        end
        turtle.turnRight()
        turtle.turnRight()
        while turtle.detect() do
            dig()
        end
        turtle.forward()
        turtle.turnRight()
    end
    turtle.turnRight()
    turtle.turnRight()
    turtle.forward()
    turtle.turnLeft()
    turtle.forward()
    turtle.turnLeft()
    turtle.forward()
    turtle.turnLeft()
    turtle.forward()
    turtle.turnRight()
end

-- Mines a 2x1 side shaft off of the main shaft of the system
function sideShaft()
    turtle.select(1)
    for i=0,10,1 do
        while turtle.detect() == true do
            dig()
        end
        turtle.forward()
        while turtle.detectUp() == true do
            turtle.digUp()
        end
    end
    turtle.turnRight()
    turtle.turnRight()
    turtle.turnRight()
    turtle.turnRight()
    turtle.select(1)
    for i=0,10,1 do
        while turtle.detect() == true do
            dig()
        end
        turtle.forward()
        while turtle.detectUp() == true do
            turtle.digUp()
        end
    end
    turtle.turnRight()
    turtle.turnRight()
    turtle.up()
    for i=1,23,1 do
        while turtle.detect() do
            dig()
        end
        turtle.forward()
    end
    turtle.down()
end


-- Places all the goodies in the designated chest
function deposit()
    for i=1, (chestDist), 1 do
        turtle.forward()
    end
    for i=1, 11, 1 do
        turtle.select(i)
        turtle.drop()
    end
    refuel()
    if turtle.getFuelLevel() < (108 + 2 * chestDist) then
        stopMining()
    end
    turtle.turnRight()
    turtle.turnRight()
    for i=1, (chestDist), 1 do
        turtle.forward()
    end

end

-- Stops mining for some reason or another
function stopMining()
    if turtle.getFuelLevel() < (108 + 2 * chestDist) then
        print("I am low on fuel.")
        local remainFuel = 0
        for i=currentPos, length, 1 do
            remainFuel = (108 + 2 * (4 * i + 1))
        end
        print("I need "..remainFuel.." to finish.")
        print("That's "..(remainFuel/80).." coal or "..(remainFuel/1000).." lava.")
        print("Type (cont) to refuel & continue mining.")
        doFuel = true
    end
    if turtle.getItemCount(16) < 6 then
        print("I am low on torches.")
        print("Place more in slot 9...")
        while turtle.getItemCount(16) < 6 do
            sleep(1)
        end
        print("Type (cont) to continue mining.")
        doFuel = false
    end
    local cont = false
    while cont == false do
        --[[
        if rs.getInput("right") == true then --Flickers RS torch on right of chest
            rs.setOutput("right", false)
        else
            rs.setOutput("right", true)
        end
        ]]
        local input = io.read()
        if input == "cont" then

            if doFuel then
                refuel()
            end

            turtle.turnRight()
            turtle.turnRight()
            for i=1, chestDist, 1 do
                turtle.forward()
            end
            currentPos = currentPos + 1
            run()
        else
            print("Incorrect input.")
        end
    end
end

-- Run the mining loop
function run()
    while currentPos < length do
        chestDist = (currentPos * 4 + 4)
        mainShaft()
        turtle.turnLeft()
        sideShaft()
        sideShaft()
        turtle.turnLeft()
        deposit()
        currentPos = currentPos + 1
    end
end

-- Alert system for user, using the redstone torch
function idle()
    print("Mining Complete")
    print("Type (end) to terminate program")
    local input = "null"
    rs.setOutput("right", true)
    while input ~= "end" do
        input = io.read()
    end
    rs.setOutput("right", false)
end

--Execution
print("----------------------------------")
print("Branch Mine Turtle Activated")
print("----------------------------------")
sleep(2)
print("Beginning Mine w. Following Specs:")
print("Main Shaft: "..mainShaftDim)
print("Side Shafts: "..sideShaftDim)
print("Branch Frequency: "..shaftFreq)
print("----------------------------------")

print("Number of Shafts:")
length = tonumber(read())
currentPos = 0
print("----------------------------------")

for x = length, 0, -1 do
    totalCost = totalCost + (108 + 2 * (4 * x + 1))
end


print("Current Fuel: "..turtle.getFuelLevel())
print("Fuel cost: "..totalCost)
print("Coal cost: "..(totalCost/80))
print("Lava cost: "..(totalCost/1000))
sleep(2)
print("----------------------------------")
print("Would you like to refuel now (y/n)?")
input = io.read()
if input == "y" then
    refuel()
    print("Refueled.")
else
    print("Did not refuel.")
end
print("Turtle now has "..turtle.getFuelLevel().." fuel.")
print("----------------------------------")

print("Now beginning mining!")

run()
turtle.turnRight()
turtle.turnRight()
for i=1, chestDist, 1 do
    turtle.forward()
end
idle()