diff --git a/test/cljam/io/cram/encode/partitioning_test.clj b/test/cljam/io/cram/encode/partitioning_test.clj
new file mode 100644
index 00000000..c988f81e
--- /dev/null
+++ b/test/cljam/io/cram/encode/partitioning_test.clj
@@ -0,0 +1,201 @@
+(ns cljam.io.cram.encode.partitioning-test
+  (:require [cljam.io.cram.encode.partitioning :as partition]
+            [clojure.test :refer [are deftest is testing]]))
+
+(defn- partition-alignments [header options alns]
+  (let [acc (volatile! [])]
+    (partition/with-each-container header options alns
+      (fn [counter container-records]
+        (vswap! acc conj [counter (mapv vec container-records)])))
+    @acc))
+
+(deftest with-each-container-test
+  (let [options {:slices-per-container 2
+                 :records-per-slice 3
+                 :min-single-ref-slice-size 2}]
+    (testing "sorted by coord"
+      (let [header {:HD {:SO "coordinate"}}]
+        (are [input expected]
+             (= expected
+                (partition-alignments header options input))
+          []
+          []
+
+          [{:qname "q1", :rname "chr1"}]
+          [[0 [[{:qname "q1", :rname "chr1"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "chr1"}
+           {:qname "q4", :rname "chr1"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}
+                {:qname "q3", :rname "chr1"}]
+               [{:qname "q4", :rname "chr1"}]]]]
+
+          (map (fn [i] {:qname (str \q (inc (long i))), :rname "chr1"}) (range 6))
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}
+                {:qname "q3", :rname "chr1"}]
+               [{:qname "q4", :rname "chr1"}
+                {:qname "q5", :rname "chr1"}
+                {:qname "q6", :rname "chr1"}]]]]
+
+          (map (fn [i] {:qname (str \q (inc (long i))), :rname "chr1"}) (range 7))
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}
+                {:qname "q3", :rname "chr1"}]
+               [{:qname "q4", :rname "chr1"}
+                {:qname "q5", :rname "chr1"}
+                {:qname "q6", :rname "chr1"}]]]
+           [6 [[{:qname "q7", :rname "chr1"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}]]]
+           [2 [[{:qname "q3", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "chr1"}
+           {:qname "q4", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}
+                {:qname "q3", :rname "chr1"}]]]
+           [3 [[{:qname "q4", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "chr2"}
+           {:qname "q4", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}]]]
+           [2 [[{:qname "q3", :rname "chr2"}
+                {:qname "q4", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr2"}
+           {:qname "q3", :rname "chr2"}
+           {:qname "q4", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr2"}]]]
+           [2 [[{:qname "q3", :rname "chr2"}
+                {:qname "q4", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "chr1"}
+           {:qname "q4", :rname "chr1"}
+           {:qname "q5", :rname "chr2"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}
+                {:qname "q3", :rname "chr1"}]
+               [{:qname "q4", :rname "chr1"}]]]
+           [4 [[{:qname "q5", :rname "chr2"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr2"}
+           {:qname "q3", :rname "chr2"}
+           {:qname "q4", :rname "chr3"}
+           {:qname "q5", :rname "chr4"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr2"}]]]
+           [2 [[{:qname "q3", :rname "chr2"}
+                {:qname "q4", :rname "chr3"}]]]
+           [4 [[{:qname "q5", :rname "chr4"}]]]]
+
+          [{:qname "q1", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "*"}
+           {:qname "q2", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "*"}
+                {:qname "q2", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "*"}
+           {:qname "q2", :rname "*"}
+           {:qname "q3", :rname "*"}
+           {:qname "q4", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "*"}
+                {:qname "q2", :rname "*"}
+                {:qname "q3", :rname "*"}]
+               [{:qname "q4", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}]]]
+           [2 [[{:qname "q3", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "chr1"}
+           {:qname "q3", :rname "*"}
+           {:qname "q4", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "chr1"}]]]
+           [2 [[{:qname "q3", :rname "*"}
+                {:qname "q4", :rname "*"}]]]]
+
+          [{:qname "q1", :rname "chr1"}
+           {:qname "q2", :rname "*"}
+           {:qname "q3", :rname "*"}
+           {:qname "q4", :rname "*"}]
+          [[0 [[{:qname "q1", :rname "chr1"}
+                {:qname "q2", :rname "*"}]]]
+           [2 [[{:qname "q3", :rname "*"}
+                {:qname "q4", :rname "*"}]]]])
+        (are [input] (thrown? Exception (partition-alignments header options input))
+          [{:qname "q1", :rname "*"}
+           {:qname "q2", :rname "chr1"}]
+
+          [{:qname "q1", :rname "*"}
+           {:qname "q2", :rname "*"}
+           {:qname "q3", :rname "chr1"}])))
+    (testing "unsorted"
+      (are [input expected]
+           (= expected (partition-alignments {:HD {:SO "unsorted"}} options input))
+        [{:qname "q1", :rname "chr1"}
+         {:qname "q2", :rname "chr2"}
+         {:qname "q3", :rname "chr1"}]
+        [[0 [[{:qname "q1", :rname "chr1"}
+              {:qname "q2", :rname "chr2"}
+              {:qname "q3", :rname "chr1"}]]]]
+
+        [{:qname "q1", :rname "chr1"}
+         {:qname "q2", :rname "chr2"}
+         {:qname "q3", :rname "chr1"}
+         {:qname "q4", :rname "chr2"}]
+        [[0 [[{:qname "q1", :rname "chr1"}
+              {:qname "q2", :rname "chr2"}
+              {:qname "q3", :rname "chr1"}]]]
+         [3 [[{:qname "q4", :rname "chr2"}]]]]
+
+        [{:qname "q1", :rname "*"}
+         {:qname "q2", :rname "chr1"}]
+        [[0 [[{:qname "q1", :rname "*"}
+              {:qname "q2", :rname "chr1"}]]]]
+
+        [{:qname "q1", :rname "*"}
+         {:qname "q2", :rname "*"}
+         {:qname "q3", :rname "chr1"}]
+        [[0 [[{:qname "q1", :rname "*"}
+              {:qname "q2", :rname "*"}
+              {:qname "q3", :rname "chr1"}]]]]))))
diff --git a/test/cljam/io/cram/encode/record_test.clj b/test/cljam/io/cram/encode/record_test.clj
index 3fda2a61..b00f0503 100644
--- a/test/cljam/io/cram/encode/record_test.clj
+++ b/test/cljam/io/cram/encode/record_test.clj
@@ -6,7 +6,8 @@
             [cljam.io.sequence :as cseq]
             [cljam.test-common :as common]
             [clojure.test :refer [are deftest is testing]]
-            [clojure.walk :as walk]))
+            [clojure.walk :as walk])
+  (:import [java.util ArrayList]))
 
 (def ^:private test-seq-resolver
   (let [seqs (with-open [r (cseq/reader common/test-fa-file)]
@@ -78,7 +79,7 @@
 
 (deftest preprocess-slice-records-test
   (let [cram-header {:SQ [{:SN "ref"}]}
-        records (object-array
+        records (ArrayList.
                  [{:rname "ref", :pos 1, :cigar "5M", :seq "AGAAT", :qual "HFHHH"
                    :options [{:RG {:type "Z", :value "rg001"}}
                              {:MD {:type "Z", :value "2C2"}}
@@ -132,7 +133,7 @@
              ::record/flag 0x0b, ::record/ref-index -1, ::record/end 10, ::record/tags-index 1
              ::record/features []}]
            (walk/prewalk #(if (.isArray (class %)) (vec %) %)
-                         records)))
+                         (vec records))))
     (is (= [[{:tag :MD, :type \Z} {:tag :NM, :type \c}]
             []]
            (:tag-dict container-ctx)))
@@ -158,7 +159,7 @@
                        :RG
                        [{:ID "rg001"}
                         {:ID "rg002"}]}
-          records (object-array
+          records (ArrayList.
                    [{:qname "q001", :flag 99, :rname "ref", :pos 1, :end 5, :mapq 0,
                      :cigar "5M", :rnext "=", :pnext 151, :tlen 150, :seq "AGAAT", :qual "HFHHH"
                      :options [{:RG {:type "Z", :value "rg001"}}
@@ -337,7 +338,7 @@
     (let [cram-header {:SQ
                        [{:SN "ref"}
                         {:SN "ref2"}]}
-          records (object-array
+          records (ArrayList.
                    [{:qname "q001", :flag 77, :rname "*", :pos 0, :end 0, :mapq 0,
                      :cigar "*", :rnext "*", :pnext 0, :tlen 0, :seq "AATCC", :qual "CCFFF"
                      :options []}