cljam.util.chromosome

(ns cljam.util.chromosome
  (:require [clojure.string :as cstr]
            [proton.core :as proton]))

(defn normalize-name
  [s]
  (-> s
      (cstr/replace #"[,\.]" "_")
      (cstr/replace #"[\"\']" )))

(defn trim-chromosome-key
  [s]
  (cstr/replace s #"(?i)^chr" ""))

(defn- split-version-suffix
  [s]
  (let [[_ base suffix _] (re-matches #"(.+?)((?i)v[0-9](_alt|_random)?)?" s)]
    [base suffix]))

(defn- normalize-chromosome-prefix
  [s]
  (if-let [[_ base leftover] (re-matches #"(?i)chr([0-9]{1,2}|X|Y|M|MT|Un)(.*)" s)]
    (let [base* (condp re-matches base
                  #"\d+" (str (Integer/parseInt base))
                  #"(?i)Un" "Un"
                  (cstr/upper-case base))]
      (str "chr" (str base* (cstr/upper-case leftover))))
    s))

(defn- prepend-chromosome-prefix
  [s]
  (if (re-matches #"(?i)([0-9]{1,2}|X|Y|M|MT|Un).*" s)
    (str "chr" s)
    s))

(defn normalize-chromosome-key
  [s]
  (let [[base version-suffix] (split-version-suffix s)]
    (str (-> base
             normalize-name
             prepend-chromosome-prefix
             normalize-chromosome-prefix)
         (when version-suffix (cstr/lower-case version-suffix)))))

(defn is-primary-chromosome?
  [s]
  (some? (re-matches #"^chr([0-9]{1,2}|X|Y|M|MT)"
                     (normalize-chromosome-key s))))

(defn chromosome-order-key [s]
  (if-let [[_ _ chr suffix] (re-find #"(?i)^(chr)?([1-9][0-9]*|X|Y|MT|M)(\S*)" s)]
    (if-let [num (proton/as-int chr)]
      [num suffix]
      [(- Integer/MAX_VALUE (case chr "X" 4 "Y" 3 "M" 2 "MT" 1)) suffix])
    [Integer/MAX_VALUE s]))