Fix bad expressions.

src/cljam/io/util/bin.clj

@@ -35,7 +35,7 @@
   (bit-shift-right (if (<= pos 0) 0 (dec pos)) linear-index-shift))
 
 (defn get-spans
-  "Calculate span information for random access from ndex data such as tabix."
+  "Calculate span information for random access from index data such as tabix."
   [index-data ^long ref-idx ^long beg ^long end]
   (let [bins (reg->bins beg end)
         chunks (get-chunks index-data ref-idx bins)

src/cljam/io/vcf/reader.clj

@@ -181,14 +181,8 @@
                     :vcf identity)]
      (map parse-fn (read-data-lines (.reader rdr) (.header rdr) kws)))))
 
-(defn- make-lazy-variants [f s]
-  (when-first [fs s]
-    (lazy-cat
-     (f fs)
-     (make-lazy-variants f (rest s)))))
-
 (defn read-variants-randomly
-  "Read variants of the  bgzip compressed VCF file randomly using tabix file.
+  "Reads variants of the bgzip compressed VCF file randomly using tabix file.
    Returning them as a lazy sequence."
   [^VCFReader rdr
    {:keys [chr start end] :or {start 1 end 4294967296}}
@@ -202,7 +196,7 @@
         parse-fn (case depth
                    :deep (vcf-util/variant-parser (.meta-info rdr) (.header rdr))
                    :vcf identity)]
-    (make-lazy-variants
+    (mapcat
      (fn [[chunk-beg ^long chunk-end]]
        (.seek input-stream chunk-beg)
        (->> #(when (< (.getFilePointer input-stream) chunk-end)

test/cljam/io/tabix_test.clj

@@ -23,8 +23,8 @@
     (is (number? (.meta tabix-data)))
     (is (number? (.skip tabix-data)))
     (is (vector? (.seq tabix-data)))
-    (is (instance?  Chunk (get (get (get (.bidx tabix-data) 0) 4687) 0)))
-    (is (vector?  (get (.lidx tabix-data) 0)))))
+    (is (instance? Chunk (get (get (get (.bidx tabix-data) 0) 4687) 0)))
+    (is (vector? (get (.lidx tabix-data) 0)))))
 
 (deftest-remote large-file
   (with-before-after {:before (prepare-cavia!)}