hamming
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{
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"authors": [
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"Teapane"
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],
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"contributors": [
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"angelikatyborska",
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"Cohen-Carlisle",
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"dalexj",
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"devonestes",
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"jedschneider",
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"lpil",
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"neenjaw",
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"parkerl",
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"percygrunwald",
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"sotojuan",
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"veelenga",
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"waiting-for-dev"
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],
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"files": {
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"solution": [
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"lib/hamming.ex"
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],
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"test": [
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"test/hamming_test.exs"
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],
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"example": [
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".meta/example.ex"
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]
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},
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"blurb": "Calculate the Hamming difference between two DNA strands.",
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"source": "The Calculating Point Mutations problem at Rosalind",
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"source_url": "https://rosalind.info/problems/hamm/"
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}
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{"track":"elixir","exercise":"hamming","id":"834311640e76451ab99f7b24cbe83404","url":"https://exercism.org/tracks/elixir/exercises/hamming","handle":"negrienko","is_requester":true,"auto_approve":false}
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# Used by "mix format"
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[
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inputs: ["{mix,.formatter}.exs", "{config,lib,test}/**/*.{ex,exs}"]
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]
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# The directory Mix will write compiled artifacts to.
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/_build/
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# If you run "mix test --cover", coverage assets end up here.
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/cover/
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# The directory Mix downloads your dependencies sources to.
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/deps/
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# Where third-party dependencies like ExDoc output generated docs.
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/doc/
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# Ignore .fetch files in case you like to edit your project deps locally.
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/.fetch
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# If the VM crashes, it generates a dump, let's ignore it too.
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erl_crash.dump
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# Also ignore archive artifacts (built via "mix archive.build").
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*.ez
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# Ignore package tarball (built via "mix hex.build").
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hamming-*.tar
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# Help
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## Running the tests
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From the terminal, change to the base directory of the exercise then execute the tests with:
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```bash
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$ mix test
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```
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This will execute the test file found in the `test` subfolder -- a file ending in `_test.exs`
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Documentation:
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* [`mix test` - Elixir's test execution tool](https://hexdocs.pm/mix/Mix.Tasks.Test.html)
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* [`ExUnit` - Elixir's unit test library](https://hexdocs.pm/ex_unit/ExUnit.html)
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## Pending tests
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In test suites of practice exercises, all but the first test have been tagged to be skipped.
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Once you get a test passing, you can unskip the next one by commenting out the relevant `@tag :pending` with a `#` symbol.
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For example:
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```elixir
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# @tag :pending
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test "shouting" do
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assert Bob.hey("WATCH OUT!") == "Whoa, chill out!"
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end
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```
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If you wish to run all tests at once, you can include all skipped test by using the `--include` flag on the `mix test` command:
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```bash
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$ mix test --include pending
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```
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Or, you can enable all the tests by commenting out the `ExUnit.configure` line in the file `test/test_helper.exs`.
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```elixir
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# ExUnit.configure(exclude: :pending, trace: true)
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```
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## Useful `mix test` options
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* `test/<FILE>.exs:LINENUM` - runs only a single test, the test from `<FILE>.exs` whose definition is on line `LINENUM`
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* `--failed` - runs only tests that failed the last time they ran
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* `--max-failures` - the suite stops evaluating tests when this number of test failures
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is reached
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* `--seed 0` - disables randomization so the tests in a single file will always be ran
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in the same order they were defined in
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## Submitting your solution
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You can submit your solution using the `exercism submit lib/hamming.ex` command.
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This command will upload your solution to the Exercism website and print the solution page's URL.
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It's possible to submit an incomplete solution which allows you to:
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- See how others have completed the exercise
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- Request help from a mentor
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## Need to get help?
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If you'd like help solving the exercise, check the following pages:
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- The [Elixir track's documentation](https://exercism.org/docs/tracks/elixir)
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- The [Elixir track's programming category on the forum](https://forum.exercism.org/c/programming/elixir)
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- [Exercism's programming category on the forum](https://forum.exercism.org/c/programming/5)
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- The [Frequently Asked Questions](https://exercism.org/docs/using/faqs)
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Should those resources not suffice, you could submit your (incomplete) solution to request mentoring.
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If you're stuck on something, it may help to look at some of the [available resources](https://exercism.org/docs/tracks/elixir/resources) out there where answers might be found.
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# Hamming
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Welcome to Hamming on Exercism's Elixir Track.
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If you need help running the tests or submitting your code, check out `HELP.md`.
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## Instructions
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Calculate the Hamming Distance between two DNA strands.
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Your body is made up of cells that contain DNA.
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Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells.
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In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!
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When cells divide, their DNA replicates too.
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Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information.
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If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred.
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This is known as the "Hamming Distance".
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We read DNA using the letters C,A,G and T.
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Two strands might look like this:
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GAGCCTACTAACGGGAT
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CATCGTAATGACGGCCT
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^ ^ ^ ^ ^ ^^
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They have 7 differences, and therefore the Hamming Distance is 7.
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The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)
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## Implementation notes
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The Hamming distance is only defined for sequences of equal length, so an attempt to calculate it between sequences of different lengths should not work.
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## Source
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### Created by
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- @Teapane
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### Contributed to by
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- @angelikatyborska
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- @Cohen-Carlisle
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- @dalexj
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- @devonestes
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- @jedschneider
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- @lpil
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- @neenjaw
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- @parkerl
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- @percygrunwald
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- @sotojuan
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- @veelenga
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- @waiting-for-dev
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### Based on
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The Calculating Point Mutations problem at Rosalind - https://rosalind.info/problems/hamm/
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defmodule Hamming do
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@doc """
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Returns number of differences between two strands of DNA, known as the Hamming Distance.
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## Examples
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iex> Hamming.hamming_distance(~c"AAGTCATA", ~c"TAGCGATC")
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{:ok, 4}
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"""
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@spec hamming_distance([char], [char]) :: {:ok, non_neg_integer} | {:error, String.t()}
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def hamming_distance(strand1, strand2) when length(strand1) != length(strand2), do: {:error, "strands must be of equal length"}
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def hamming_distance(strand1, strand2) do
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{:ok, Enum.count(Enum.zip(strand1, strand2), fn {s1, s2} -> s1 != s2 end)}
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end
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end
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defmodule Hamming.MixProject do
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use Mix.Project
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def project do
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[
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app: :hamming,
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version: "0.1.0",
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# elixir: "~> 1.8",
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start_permanent: Mix.env() == :prod,
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deps: deps()
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]
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end
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# Run "mix help compile.app" to learn about applications.
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def application do
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[
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extra_applications: [:logger]
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]
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end
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# Run "mix help deps" to learn about dependencies.
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defp deps do
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[
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# {:dep_from_hexpm, "~> 0.3.0"},
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# {:dep_from_git, git: "https://github.com/elixir-lang/my_dep.git", tag: "0.1.0"}
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]
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end
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end
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defmodule HammingTest do
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use ExUnit.Case
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test "empty strands" do
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assert Hamming.hamming_distance(~c"", ~c"") == {:ok, 0}
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end
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test "single letter identical strands" do
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assert Hamming.hamming_distance(~c"A", ~c"A") == {:ok, 0}
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end
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test "single letter different strands" do
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assert Hamming.hamming_distance(~c"G", ~c"T") == {:ok, 1}
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end
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test "long identical strands" do
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assert Hamming.hamming_distance(~c"GGACTGAAATCTG", ~c"GGACTGAAATCTG") == {:ok, 0}
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end
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test "long different strands" do
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assert Hamming.hamming_distance(~c"GGACGGATTCTG", ~c"AGGACGGATTCT") == {:ok, 9}
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end
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test "disallow first strand longer" do
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assert {:error, "strands must be of equal length"} =
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Hamming.hamming_distance(~c"AATG", ~c"AAA")
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end
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test "disallow second strand longer" do
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assert {:error, "strands must be of equal length"} =
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Hamming.hamming_distance(~c"ATA", ~c"AGTG")
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end
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test "disallow empty first strand" do
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assert {:error, "strands must be of equal length"} = Hamming.hamming_distance(~c"", ~c"G")
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end
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test "disallow empty second strand" do
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assert {:error, "strands must be of equal length"} = Hamming.hamming_distance(~c"G", ~c"")
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end
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end
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ExUnit.start()
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ExUnit.configure(exclude: :pending, trace: true)
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