Add utilities for whole-genome coordinate.

src/cljam/util/whole_genome.clj

@@ -0,0 +1,53 @@
+(ns cljam.util.whole-genome
+  "Utilities for conversions between chromosomal positions and whole-genome positions.")
+
+(defn create-chr-to-whole-genome-index
+  "Creates a map of [chromosome-name offset&length] from refs."
+  [refs]
+  (->> refs
+       (map :len)
+       (reductions + 0)
+       (map (fn [r offset] [(:name r) {:offset offset, :len (:len r)}]) refs)
+       (into {})))
+
+(defn to-whole-genome-coord
+  "Transforms a position in a chromosome into a whole-genome position."
+  [chr->offset chr ^long pos]
+  (when-let [{:keys [^long offset ^long len]} (chr->offset chr)]
+    (when (<= 1 pos len)
+      (inc (+ offset (dec pos))))))
+
+(defn create-whole-genome-to-chr-index
+  "Creates a sorted-map of [offset chromosome-name&length] from refs."
+  [refs]
+  (into (sorted-map)
+        (map vector
+         (->> refs
+              (map :len)
+              (reductions + 0))
+         refs)))
+
+(defn to-chr-and-pos
+  "Transforms a whole-genome position to a vector of a chromosome name and a position in the chromosome."
+  [offset->ref ^long wg-pos]
+  (when-let [[^long offset {:keys [name len]}] (first (rsubseq offset->ref <= (dec wg-pos)))]
+    (when (<= 1 (- wg-pos offset) len)
+      [name (- wg-pos offset)])))
+
+(defn to-regions
+  "Transforms a region in whole-genome coordinate into a sequence of chromosomal regions."
+  [offset->ref ^long start ^long end]
+  (let [wg-len (let [[o r] (first (rsubseq offset->ref > 0))] (+ o (:len r)))]
+    (when (and (<= start end) (or (pos? start) (pos? end)) (or (<= start wg-len) (<= end wg-len)))
+      (let [start' (min (max 1 start) wg-len)
+            end' (min (max 1 end) wg-len)
+            [s-offset {s-name :name s-len :len}] (first (rsubseq offset->ref <= (dec start')))
+            [e-offset {e-name :name e-len :len}] (first (rsubseq offset->ref <= (dec end')))]
+        (if (= s-offset e-offset)
+          [{:chr s-name, :start (- start' s-offset), :end (min (- end' s-offset) s-len)}]
+          (concat
+           [{:chr s-name, :start (- start' s-offset), :end s-len}]
+           (map
+            (fn [[_ r]] {:chr (:name r), :start 1, :end (:len r)})
+            (subseq offset->ref > s-offset < e-offset))
+           [{:chr e-name, :start 1, :end (min (- end' e-offset) e-len)}]))))))

test/cljam/util/t_whole_genome.clj

@@ -0,0 +1,82 @@
+(ns cljam.util.t-whole-genome
+  (:require [clojure.test :refer :all]
+            [cljam.util.whole-genome :as wg]))
+
+(def simple-refs [{:name "1", :len 100} {:name "2", :len 200} {:name "3", :len 300}])
+(def refs
+  [{:name "chr1", :len 248956422}  {:name "chr2", :len 242193529}  {:name "chr3", :len 198295559}
+   {:name "chr4", :len 190214555}  {:name "chr5", :len 181538259}  {:name "chr6", :len 170805979}
+   {:name "chr7", :len 159345973}  {:name "chr8", :len 145138636}  {:name "chr9", :len 138394717}
+   {:name "chr10", :len 133797422} {:name "chr11", :len 135086622} {:name "chr12", :len 133275309}
+   {:name "chr13", :len 114364328} {:name "chr14", :len 107043718} {:name "chr15", :len 101991189}
+   {:name "chr16", :len 90338345}  {:name "chr17", :len 83257441}  {:name "chr18", :len 80373285}
+   {:name "chr19", :len 58617616}  {:name "chr20", :len 64444167}  {:name "chr21", :len 46709983}
+   {:name "chr22", :len 50818468}  {:name "chrX", :len 156040895}  {:name "chrY", :len 57227415}
+   {:name "chrM", :len 16569}])
+
+(deftest chr->wg
+  (let [idx (wg/create-chr-to-whole-genome-index simple-refs)]
+    (testing "chr -> whole-genome index"
+      (is (= idx {"1" {:offset 0, :len 100}, "2" {:offset 100, :len 200}, "3" {:offset 300, :len 300}})))
+
+    (testing "chr -> whole-genome (simple)"
+      (are [?chr ?pos ?wg-pos]
+          (= (wg/to-whole-genome-coord idx ?chr ?pos) ?wg-pos)
+        "0" 1 nil
+        "1" 0 nil
+        "1" 1 1
+        "1" 100 100
+        "2" 0 nil
+        "2" 1 101
+        "2" 200 300
+        "2" 201 nil
+        "3" 1 301
+        "3" 300 600
+        "3" 301 nil)))
+
+  (let [idx (wg/create-chr-to-whole-genome-index refs)]
+    (testing "chr -> whole-genome"
+      (are [?chr ?pos ?wg-pos]
+          (= (wg/to-whole-genome-coord idx ?chr ?pos) ?wg-pos)
+        "chr1" 1 1
+        "chr1" 248956422 248956422
+        "chr2" 1 (+ 248956422 1)
+        "chr2" 242193529 (+ 248956422 242193529)
+        "chr3" 1 (+ 248956422 242193529 1)))))
+
+(deftest wg->chr
+  (let [idx (wg/create-whole-genome-to-chr-index simple-refs)]
+    (testing "whole-genome -> chr index"
+      (is (= idx {0 {:name "1", :len 100}, 100 {:name "2", :len 200}, 300 {:name "3", :len 300}})))
+
+    (testing "whole-genome -> chr"
+      (are [?wg-pos ?chr-and-pos]
+          (= (wg/to-chr-and-pos idx ?wg-pos) ?chr-and-pos)
+          0 nil
+          1 ["1" 1]
+          2 ["1" 2]
+          99 ["1" 99]
+          100 ["1" 100]
+          101 ["2" 1]
+          300 ["2" 200]
+          301 ["3" 1]
+          600 ["3" 300]
+          601 nil))
+
+    (testing "whole-genome [start, end] -> regions"
+      (are [?wg-start ?wg-end ?regions]
+          (= (wg/to-regions idx ?wg-start ?wg-end) ?regions)
+        0 0 nil
+        0 1 [{:chr "1", :start 1, :end 1}]
+        1 0 nil
+        1 1 [{:chr "1", :start 1, :end 1}]
+        1 2 [{:chr "1", :start 1, :end 2}]
+        2 1 nil
+        50 100 [{:chr "1", :start 50, :end 100}]
+        50 150 [{:chr "1", :start 50, :end 100} {:chr "2", :start 1, :end 50}]
+        50 350 [{:chr "1", :start 50, :end 100} {:chr "2", :start 1, :end 200} {:chr "3", :start 1, :end 50}]
+        150 550 [{:chr "2", :start 50, :end 200} {:chr "3", :start 1, :end 250}]
+        301 600 [{:chr "3", :start 1, :end 300}]
+        301 601 [{:chr "3", :start 1, :end 300}]
+        600 601 [{:chr "3", :start 300, :end 300}]
+        601 601 nil))))