Change validator structure of base records.

chrovis · Jul 19, 2023 · 0a03b50 · 0a03b50
1 parent 0f78812
commit 0a03b50
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Showing 2 changed files with 29 additions and 31 deletions.
diff --git a/src/cljam/io/vcf/util/validator.clj b/src/cljam/io/vcf/util/validator.clj
@@ -17,36 +17,30 @@
            (every? keyword? filt))))
 
 (defn- check-base-records [variant meta-included-contig? meta-included-format?]
-  (cond-> nil
-    (some #{\< \> \, \space \tab} (:chr variant))
-    (update :chr (fnil conj []) "Must not contain whitespaces commas or angle brackets.")
-
-    (not (meta-included-contig? (:chr variant)))
-    (update :chr (fnil conj []) "Must be contained in contig header.")
-
-    (not (integer? (:pos variant)))
-    (update :pos (fnil conj []) "Position must be Integer.")
-
-    (not (valid-ref? (:ref variant)))
-    (update :ref (fnil conj []) "Not include invalid char.")
-
-    (and (seq (:alt variant))
-         (not (sequential? (:alt variant))))
-    (update :alt (fnil conj []) "Must be sequence.")
-
-    (and (sequential? (:alt variant))
-         (not (every? #(vcf-util/inspect-allele % (:ref variant))
-                      (:alt variant))))
-    (update :alt (fnil conj []) "Invalid allele.")
-
-    (not (valid-qual? (:qual variant)))
-    (update :qual (fnil conj []) "Qual must be float.")
-
-    (not (valid-filter? (:filter variant)))
-    (update :filter (fnil conj []) "Invalid filter.")
-
-    (not (meta-included-format? (:format variant)))
-    (update :format (fnil conj []) "Must be contain meta")))
+  (reduce-kv
+   (fn [m k vs]
+     (reduce
+      (fn [m [pred msg]]
+        (cond-> m (not (pred (k variant))) (update k (fnil conj []) msg)))
+      m
+      vs))
+   nil
+   {:chr
+    [[(complement (partial some #{\< \> \, \space \tab}))
+      "Must not contain whitespaces commas or angle brackets."]
+     [meta-included-contig? (format (str "CHROM %s must be declared in a "
+                                         "##contig field in the header.")
+                                    (:chr variant))]],
+    :pos [[integer? "Position must be Integer."]],
+    :ref [[valid-ref? "Not include invalid char."]]
+    :alt [[(some-fn (complement seq) sequential?) "Must be sequence."]
+          [(some-fn
+            (complement sequential?)
+            (partial every? #(vcf-util/inspect-allele % (:ref variant))))
+           "Invalid allele."]]
+    :qual [[valid-qual? "Qual must be float."]]
+    :filter [[valid-filter? "Invalid filter."]]
+    :format [[meta-included-format? "Must be contain meta"]]}))
 
 (defn- check-entry-type [entry type-str]
   ((case type-str

diff --git a/test/cljam/io/vcf/util/validator_test.clj b/test/cljam/io/vcf/util/validator_test.clj
@@ -77,7 +77,11 @@
              {:chr "c hr10" :pos 10}
              {:contig [{:id "c hr10"}]}
              base-header))
-           ["Must not contain whitespaces commas or angle brackets."])))
+           ["Must not contain whitespaces commas or angle brackets."]))
+    (is (= (:chr
+            (validator/invalid-variant?  {:chr "chr10" :pos 10}
+                                        {} base-header))
+           ["CHROM chr10 must be declared in a ##contig field in the header."])))
   (testing "ref check"
     (is (= (:ref
             (validator/invalid-variant?