wip: Throw error if reference embedding target CRAM is not sorted

chrovis · Oct 10, 2024 · de3fc6a · de3fc6a
1 parent 2ccd5a5
commit de3fc6a
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Showing 2 changed files with 54 additions and 26 deletions.
diff --git a/src/cljam/io/cram/writer.clj b/src/cljam/io/cram/writer.clj
@@ -42,13 +42,21 @@
 (defn write-header
   "Writes the CRAM header."
   [^CRAMWriter wtr header]
-  (when (and (.-index-writer wtr)
-             (not (:skip-sort-order-check? (.-options wtr)))
-             (not= (sam.header/sort-order header) sam.header/order-coordinate))
-    (throw
-     (ex-info "Cannot create CRAM index file for CRAM file not declared as sorted by coordinate"
-              {:sort-order (sam.header/sort-order header)})))
-  (struct/encode-cram-header-container (.-stream wtr) header))
+  (let [opts (.-options wtr)
+        sort-order (sam.header/sort-order header)]
+    (when (and (not (= sort-order sam.header/order-coordinate))
+               (not (:skip-sort-order-check? opts)))
+      (when (.-index-writer wtr)
+        (throw
+         (ex-info (str "Cannot create CRAM index file for CRAM file not declared "
+                       "as sorted by coordinate")
+                  {:sort-order sort-order})))
+      (when (:embed-reference? opts)
+        (throw
+         (ex-info (str "Cannot embed reference sequences for CRAM file not declared "
+                       "as sorted by coordinate")
+                  {:sort-order sort-order}))))
+    (struct/encode-cram-header-container (.-stream wtr) header)))
 
 (defn- preprocess-records
   [cram-header seq-resolver options ^objects container-records]

diff --git a/test/cljam/io/cram_test.clj b/test/cljam/io/cram_test.clj
@@ -143,25 +143,45 @@
 (deftest writer-with-reference-embedding-test
   (with-before-after {:before (prepare-cache!)
                       :after (clean-cache!)}
-    (with-open [r (cram/reader common/test-sorted-cram-file
-                               {:reference common/test-fa-file})
-                w (cram/writer temp-sorted-cram-file
-                               {:reference common/test-fa-file
-                                :embed-reference? true
-                                :ds-compressor-overrides {:embedded-ref :raw}})]
-      (cram/write-header w (cram/read-header r))
-      (cram/write-alignments w (cram/read-alignments r) (cram/read-header r)))
-    (with-open [r (cram/reader common/test-sorted-cram-file
-                               {:reference common/test-fa-file})
-                r' (cram/reader temp-sorted-cram-file)]
-      (is (= (cram/read-header r)
-             (cram/read-header r')))
-      (is (= (cram/read-alignments r)
-             (cram/read-alignments r'))))
-    (with-open [r (cram/reader temp-sorted-cram-file)]
-      (let [headers (all-compression-headers r)]
-        (is (seq headers))
-        (is (every? #(false? (get-in % [:preservation-map :RR])) headers))))))
+    (testing "Reference embedding will be enabled if `:embed-reference?` is set to true"
+      (with-open [r (cram/reader common/test-sorted-cram-file
+                                 {:reference common/test-fa-file})
+                  w (cram/writer temp-sorted-cram-file
+                                 {:reference common/test-fa-file
+                                  :embed-reference? true
+                                  :skip-sort-order-check? true
+                                  :ds-compressor-overrides {:embedded-ref :raw}})]
+        (cram/write-header w (cram/read-header r))
+        (cram/write-alignments w (cram/read-alignments r) (cram/read-header r)))
+      (with-open [r (cram/reader common/test-sorted-cram-file
+                                 {:reference common/test-fa-file})
+                  r' (cram/reader temp-sorted-cram-file)]
+        (is (= (cram/read-header r)
+               (cram/read-header r')))
+        (is (= (cram/read-alignments r)
+               (cram/read-alignments r'))))
+      (with-open [r (cram/reader temp-sorted-cram-file)]
+        (let [headers (all-compression-headers r)]
+          (is (seq headers))
+          (is (every? #(false? (get-in % [:preservation-map :RR])) headers)))))
+    (testing "Error when trying to embed reference sequences for a CRAM file not declared as `SO:coordinate`"
+      (with-open [r (cram/reader common/test-sorted-with-unknown-so-cram-file
+                                 {:reference common/test-fa-file})
+                  w (cram/writer temp-cram-file
+                                 {:reference common/test-fa-file
+                                  :embed-reference? true
+                                  :ds-compressor-overrides {:embedded-ref :raw}})]
+        (is (thrown-with-msg? Exception #"Cannot embed reference sequences for CRAM file not declared as sorted by coordinate"
+                              (cram/write-header w (cram/read-header r))))))
+    (testing "`:skip-sort-order-check?` skips the header check when embedding reference sequences"
+      (with-open [r (cram/reader common/test-sorted-with-unknown-so-cram-file
+                                 {:reference common/test-fa-file})
+                  w (cram/writer temp-cram-file
+                                 {:reference common/test-fa-file
+                                  :embed-reference? true
+                                  :skip-sort-order-check? true
+                                  :ds-compressor-overrides {:embedded-ref :raw}})]
+        (is (any? (cram/write-header w (cram/read-header r))))))))
 
 (deftest writer-index-options-test
   (with-before-after {:before (prepare-cache!)