refactor: refactor and generalize overlap-exon-intron-boundary? using diff-bases

Author: federkasten

src/varity/vcf_to_hgvs/protein.clj

@@ -14,20 +14,23 @@
             [varity.ref-gene :as rg]
             [varity.vcf-to-hgvs.common :refer [diff-bases] :as common]))
 
-(defn- overlap-exon-intron-boundary?
+(defn- overlap-exon-intron-boundary?*
   [exon-ranges pos ref alt]
   (let [nref (count ref)
-        nalt (count alt)]
-    (and (not (= 1 nref nalt))
-         (not= 1 (count exon-ranges))
-         (let [[pos nref] (if (= (first ref) (first alt))
-                            [(inc pos) (dec nref)]
-                            [pos nref])]
-           (some (fn [[s e]]
-                   (and (not= s e)
-                        (or (and (< pos s) (<= s (+ pos nref -1)))
-                            (and (<= pos e) (< e (+ pos nref -1))))))
-                 exon-ranges)))))
+        nalt (count alt)
+        [_ _ d _] (diff-bases ref alt)
+        pos (+ pos d)
+        nref (- nref d)]
+    (boolean
+     (and (not (= 1 nref nalt))
+          (not= 1 (count exon-ranges))
+          (some (fn [[s e]]
+                  (and (not= s e)
+                       (or (and (< pos s) (<= s (+ pos nref -1)))
+                           (and (<= pos e) (< e (+ pos nref -1))))))
+                exon-ranges)))))
+
+(def ^:private overlap-exon-intron-boundary? (memoize overlap-exon-intron-boundary?*))
 
 (defn alt-exon-ranges
   "Returns exon ranges a variant applied."

test/varity/vcf_to_hgvs/protein_test.clj

@@ -7,6 +7,17 @@
             [varity.t-common :refer [test-ref-seq-file
                                      defslowtest]]))
 
+(deftest overlap-exon-intron-boundary?-test
+  (let [exon-ranges [[123 321] [456 654] [789 987]]]
+    (are [p pos ref alt] (p (#'prot/overlap-exon-intron-boundary? exon-ranges pos ref alt))
+      false? 454 "X" "Y"
+      true? 454 "XXX" "X"
+      false? 455 "XX" "X"
+      false? 456 "XX" "X"
+      false? 654 "XX" "X"
+      true? 653 "XXX" "X"
+      false? 653 "XX" "X")))
+
 (deftest alt-exon-ranges-test
   ;; 1 [2 3 4] 5 6 7 [8 9 10 11] 12 13 14 15
   (are [p r a e] (= (#'prot/alt-exon-ranges [[2 4] [8 11]] p r a) e)
@@ -15,10 +26,10 @@
     2 "XX" "X" [[2 3] [7 10]]
     3 "XX" "X" [[2 3] [7 10]]
     6 "XX" "X" [[2 4] [7 10]]
-    9 "XXX" "XXX" [[2 4] [8 11]])
+    9 "XXX" "YYY" [[2 4] [8 11]])
   ;; Variants overlapping a boundary of exon/intron
   (are [p r a] (nil? (#'prot/alt-exon-ranges [[2 4] [8 11]] p r a))
-    3 "XXX" "XXX"
+    3 "XXX" "YYY"
     6 "XXX" "X"
     3 "XXX" "X"
     1 "XXXXX" "X"))