Fix warnings and errors reported by clj-kondo

.clj-kondo/config.edn

@@ -0,0 +1,23 @@
+{:linters
+ {:type-mismatch
+  {:namespaces
+   {clojure.core
+    {long {:arities {1 {:args [#{:byte :number :char}],
+                        :ret :int}}}},
+    cljam.algo.pileup
+    {unzip-2 {:arities {1 {:args [:fn],
+                           :ret :transducer}}}}}},
+  :unresolved-symbol
+  {:exclude [(cljam.io.pileup-test/with-string-writer [w])
+             ;; cljam.algo.depth
+             (com.climate.claypoole/pdoseq [s e])
+             ;; cljam.algo.level
+             (com.climate.claypoole/pfor [i])]}},
+ :lint-as {cljam.test-common/deftest-slow clojure.test/deftest,
+           cljam.test-common/deftest-remote clojure.test/deftest,
+           cljam.util/with-temp-dir clojure.core/with-open,
+           cavia.core/defprofile clojure.core/def,
+           libra.bench/defbench clojure.test/deftest,
+           libra.bench/is clojure.test/is,
+           libra.bench/are clojure.test/are,
+           com.climate.claypoole/with-shutdown! clojure.core/with-open}}

.gitignore

@@ -13,3 +13,4 @@ pom.xml.asc
 .nrepl-port
 /.cavia
 /docs
+.clj-kondo/.cache

bench/cljam/algo/bam_indexer_bench.clj

@@ -1,5 +1,5 @@
 (ns cljam.algo.bam-indexer-bench
-  (:require [libra.bench :refer :all]
+  (:require [libra.bench :refer [defbench are dur]]
             [libra.criterium :as c]
             [cljam.test-common :as tcommon]
             [cljam.algo.bam-indexer :as bai]))

bench/cljam/algo/convert_bench.clj

@@ -1,5 +1,5 @@
 (ns cljam.algo.convert-bench
-  (:require [libra.bench :refer :all]
+  (:require [libra.bench :refer [defbench are]]
             [libra.criterium :as c]
             [cljam.test-common :as tcommon]
             [cljam.algo.convert :as convert]))

bench/cljam/algo/depth_bench.clj

@@ -1,5 +1,5 @@
 (ns cljam.algo.depth-bench
-  (:require [libra.bench :refer :all]
+  (:require [libra.bench :refer [defbench are dur]]
             [libra.criterium :as c]
             [cljam.test-common :as tcommon]
             [cljam.algo.depth :as depth]

bench/cljam/algo/pileup_bench.clj

@@ -1,5 +1,5 @@
 (ns cljam.algo.pileup-bench
-  (:require [libra.bench :refer :all]
+  (:require [libra.bench :refer [defbench is]]
             [libra.criterium :as c]
             [criterium.core :as criterium]
             [cljam.test-common :as tcommon]
@@ -15,4 +15,3 @@
           (is
            (c/quick-bench
             (dorun (pileup/pileup r region)))))))))
-

bench/cljam/io/sequence_bench.clj

@@ -1,5 +1,5 @@
 (ns cljam.io.sequence-bench
-  (:require [libra.bench :refer :all]
+  (:require [libra.bench :refer [defbench are]]
             [libra.criterium :as c]
             [cljam.test-common :as tcommon]
             [cljam.io.sequence :as cseq]))

src/cljam/algo/sorter.clj

@@ -1,15 +1,14 @@
 (ns cljam.algo.sorter
   "Sorter of the SAM/BAM format alignments."
   (:refer-clojure :exclude [sorted?])
-  (:require [clojure.java.io :as cio]
-            [clojure.tools.logging :as logging]
+  (:require [clojure.tools.logging :as logging]
             [com.climate.claypoole :as cp]
             [cljam.io.protocols :as protocols]
             [cljam.io.sam :as sam]
             [cljam.io.util :as io-util]
             [cljam.util :as util]
             [cljam.io.sam.util.header :as header])
-  (:import [java.io Closeable File]
+  (:import [java.io Closeable]
            [java.util PriorityQueue]))
 
 (def ^:const default-chunk-size 1500000)

src/cljam/io/bam/reader.clj

@@ -6,9 +6,8 @@
             [cljam.io.bam-index.core :as bai]
             [cljam.io.bam.decoder :as decoder]
             [cljam.io.util.lsb :as lsb])
-  (:import [java.io Closeable EOFException IOException FileNotFoundException]
+  (:import [java.io Closeable FileNotFoundException]
            [cljam.io.bam.decoder BAMRawBlock]
-           [java.nio ByteBuffer]
            [bgzf4j BGZFInputStream]))
 
 (declare read-blocks-sequentially*

src/cljam/io/bam_index/core.clj

@@ -70,7 +70,7 @@
   (with-open [w (writer f refs)]
     (try
       (writer/write-index! w alns)
-      (catch Exception e (do
-                           (cio/delete-file (.url w))
-                           (logging/error "Failed to create BAM index")
-                           (throw e))))))
+      (catch Exception e
+        (cio/delete-file (.url w))
+        (logging/error "Failed to create BAM index")
+        (throw e)))))

src/cljam/io/bam_index/writer.clj

@@ -4,11 +4,13 @@
             [cljam.io.util.bgzf :as bgzf]
             [cljam.io.util.lsb :as lsb]
             [cljam.io.util.bin :as util-bin]
-            [cljam.io.bam-index.common :refer :all]
+            [cljam.io.bam-index.common :refer [linear-index-shift
+                                               linear-index-depth
+                                               max-bins
+                                               bai-magic]]
             [cljam.io.util.chunk :as chunk]
             [cljam.io.bam.decoder :as bam-decoder])
   (:import [java.io DataOutputStream Closeable]
-           [java.nio ByteBuffer ByteOrder]
            [cljam.io.bam.decoder BAMPointerBlock]
            [cljam.io.util.chunk Chunk]))
 

src/cljam/io/bcf/writer.clj

@@ -6,7 +6,7 @@
             [cljam.io.vcf.writer :as vw]
             [cljam.io.vcf.util :as vcf-util]
             [cljam.util :as util])
-  (:import [java.io Closeable IOException DataOutputStream]
+  (:import [java.io Closeable DataOutputStream]
            [java.net URL]
            [java.nio ByteBuffer ByteOrder]))
 
@@ -27,7 +27,6 @@
   [:fileformat :file-date :source :reference :contig :phasing :info :filter
    :format :alt :sample :pedigree])
 (def ^:private ^:const meta-info-prefix "##")
-(def ^:private ^:const header-prefix "#")
 (def ^:private ^:const type-kws
   {"String" :str, "Character" :char,
    "Integer" :int, "Float" :float, "Flag" :flag})

src/cljam/io/bed.clj

@@ -3,7 +3,7 @@
   http://genome.ucsc.edu/FAQ/FAQformat#format1 for the detail BED specifications."
   (:require [clojure.java.io :as cio]
             [clojure.string :as cstr]
-            [proton.core :refer [as-int as-long]]
+            [proton.core :refer [as-long]]
             [cljam.io.protocols :as protocols]
             [cljam.util :as util]
             [cljam.util.chromosome :as chr]

src/cljam/io/bigwig.clj

@@ -301,8 +301,9 @@
                            end-base (lsb/read-uint r)
                            offset (lsb/read-long r)
                            size (lsb/read-long r)]
-                       (if (cir-tree-overlaps? id start end start-chrom-ix
-                                               start-base end-chrom-ix end-base)
+                       (when (cir-tree-overlaps?
+                              id start end start-chrom-ix
+                              start-base end-chrom-ix end-base)
                          {:offset offset, :size size}))))
        (remove nil?)))
 

src/cljam/io/dict/core.clj

@@ -28,7 +28,7 @@
   (with-open [w (writer f)]
     (try
       (writer/write-dict! w headers sequences ur)
-      (catch Exception e (do
-                           (cio/delete-file (.url w))
-                           (logging/error "Failed to create dictionary")
-                           (throw e))))))
+      (catch Exception e
+        (cio/delete-file (.url w))
+        (logging/error "Failed to create dictionary")
+        (throw e)))))

src/cljam/io/dict/writer.clj

@@ -47,7 +47,7 @@
 (defn make-dict
   "Calculates sequence dictionary from the headers and sequences, returning it
   as a map."
-  [headers sequences ur]
+  [_headers sequences ur]
   (loop [[seq* & rest] sequences
          name (:name seq*)
          dict-status (init-dict-status)

src/cljam/io/fasta_index/core.clj

@@ -23,10 +23,10 @@
               w ^FAIWriter (writer out-fai)]
     (try
       (writer/write-index! r w)
-      (catch Exception e (do
-                           (cio/delete-file (.url w))
-                           (logging/error "Failed to create FASTA index")
-                           (throw e))))))
+      (catch Exception e
+        (cio/delete-file (.url w))
+        (logging/error "Failed to create FASTA index")
+        (throw e)))))
 
 ;;;; Reading
 

src/cljam/io/pileup.clj

@@ -136,19 +136,19 @@
       (.append w (if reverse? \, \.))
       (.append w (unchecked-char (case-base-fn base))))
     (when deletion
-      (do (.append w \-)
-          (.append w (String/valueOf ^int deletion))
-          (.append w ^String (case-fn
-                              (if ref-reader
-                                (->> {:chr rname
-                                      :start (inc ref-pos)
-                                      :end (+ ref-pos deletion)}
-                                     (cseq/read-sequence ref-reader))
-                                (apply str (repeat deletion \N)))))))
+      (.append w \-)
+      (.append w (String/valueOf ^int deletion))
+      (.append w ^String (case-fn
+                          (if ref-reader
+                            (->> {:chr rname
+                                  :start (inc ref-pos)
+                                  :end (+ ref-pos deletion)}
+                                 (cseq/read-sequence ref-reader))
+                            (apply str (repeat deletion \N))))))
     (when insertion
-      (do (.append w \+)
-          (.append w (String/valueOf (count insertion)))
-          (.append w ^String (case-fn insertion))))
+      (.append w \+)
+      (.append w (String/valueOf (count insertion)))
+      (.append w ^String (case-fn insertion)))
     (when end?
       (.append w \$))))
 

src/cljam/io/sam/util.clj

@@ -5,9 +5,7 @@
             [cljam.io.sam.util.cigar :as cigar]
             [cljam.io.util.bin :as util-bin]
             [cljam.io.sam.util.option :as opt])
-  (:import [java.nio CharBuffer ByteBuffer]
-           [java.nio.charset StandardCharsets]
-           [cljam.io.protocols SAMAlignment]))
+  (:import [cljam.io.protocols SAMAlignment]))
 
 (def ^:const linear-index-shift 14)
 (def ^:const linear-index-depth 5)

src/cljam/io/sam/util/refs.clj

@@ -32,4 +32,4 @@
 (defn ref-by-name
   "Returns the first reference which has the specified name."
   [refs name]
-  (some #(if (= (:name %) name) %) refs))
+  (some #(when (= (:name %) name) %) refs))

src/cljam/io/sam/util/sequence.clj

@@ -33,7 +33,7 @@
         result-len (quot (inc length) 2)
         in-bb (ByteBuffer/wrap b)
         out-bb (ByteBuffer/allocate result-len)]
-    (dotimes [i result-len]
+    (dotimes [_ result-len]
       (let [u (.get in-bb)
             l (byte (if (.hasRemaining in-bb) (.get in-bb) \=))]
         (->> (bit-and 0x7F l)

src/cljam/io/twobit/writer.clj

@@ -76,14 +76,6 @@
             (recur (conj! r [p l]) nil nil (inc i))
             (recur r nil nil (inc i))))))))
 
-(defn- index-size
-  "Number of bytes required for index."
-  [seqs]
-  (-> (fn [{:keys [name]}]
-        (+ 1 (count name) 4))
-      map
-      (transduce + 0 seqs)))
-
 (defn- write-index!
   [w idx]
   (loop [offset (+ (* 4 4) (reduce + (map #(+ 1 (count (:name %)) 4) idx)))
@@ -173,7 +165,7 @@
             seq-data (or (:seq sequence) (:sequence sequence))
             masks (mask-regions seq-data)
             ambs (amb-regions seq-data)
-            i (first (keep-indexed #(if (= (:name %2) name) %1) @idx-atom))]
+            i (first (keep-indexed #(when (= (:name %2) name) %1) @idx-atom))]
         (swap! idx-atom update i assoc :masks masks :ambs ambs))
       (write-sequence! (.writer wtr) sequence @idx-atom))
     ;; finalize

src/cljam/io/util/lsb.clj

@@ -1,7 +1,7 @@
 (ns cljam.io.util.lsb
   "Reading/writing functions of stream and buffer for little-endian data."
   (:refer-clojure :exclude [read-string])
-  (:require [cljam.util :refer [string->bytes bytes->string]])
+  (:require [cljam.util :refer [string->bytes]])
   (:import [java.io DataInput InputStream DataOutputStream EOFException ByteArrayOutputStream]
            [java.nio Buffer ByteBuffer ByteOrder]))
 

src/cljam/io/vcf.clj

@@ -18,8 +18,7 @@
            cljam.io.vcf.reader.VCFReader
            cljam.io.vcf.writer.VCFWriter
            cljam.io.bcf.reader.BCFReader
-           cljam.io.bcf.writer.BCFWriter
-           bgzf4j.BGZFInputStream))
+           cljam.io.bcf.writer.BCFWriter))
 
 ;; Reading
 ;; -------
@@ -37,7 +36,7 @@
                   (bgzf/bgzf-input-stream f)
                   (cio/reader (util/compressor-input-stream f)))
                 (delay (try (csi/read-index (str f ".csi"))
-                            (catch FileNotFoundException e
+                            (catch FileNotFoundException _
                               (tabix/read-index (str f ".tbi"))))))))
 
 (defn ^BCFReader bcf-reader

src/cljam/io/vcf/writer.clj

@@ -148,7 +148,7 @@
 
 (defn- write-meta-info1
   [^VCFWriter wtr k v]
-  (if-not (nil? v)
+  (when-not (nil? v)
     (if (sequential? v)
       (doseq [x v]
         (write-line (.writer wtr) (str meta-info-prefix
@@ -182,12 +182,12 @@
 
 (defn- stringify-data-line-alt
   [v]
-  (if v
+  (when v
     (cstr/join \, v)))
 
 (defn- stringify-data-line-qual
   [x]
-  (if x
+  (when x
     (if (zero? (mod x 1))
       (str (int x))
       (str x))))

src/cljam/io/wig.clj

@@ -169,9 +169,7 @@
                                        #(- (:end %) (:start %))))
                    (map
                     (fn [[{{:keys [line format span step]} :track
-                           chr :chr
-                           start :start
-                           end :end} :as xs]]
+                           chr :chr start :start} :as xs]]
                       (case format
                         :variable-step
                         (let [declaration-line (->> (cond-> ["variableStep"

src/cljam/tools/cli.clj

@@ -323,7 +323,7 @@
 
 ;; ### version command
 
-(defn version [args]
+(defn version [_]
   (let [ver (with-open [r (-> "META-INF/maven/cljam/cljam/pom.properties"
                               (clojure.java.io/resource)
                               (clojure.java.io/reader))]

src/cljam/util.clj

@@ -1,6 +1,6 @@
 (ns cljam.util
   "General utilities."
-  (:require [clojure.java.io :refer [file] :as cio])
+  (:require [clojure.java.io :as cio])
   (:import [java.net MalformedURLException URL]
            [java.nio.file Files FileVisitor FileVisitResult]
            [java.nio.file.attribute FileAttribute]

src/cljam/util/chromosome.clj

@@ -43,7 +43,7 @@
              normalize-name
              prepend-chromosome-prefix
              normalize-chromosome-prefix)
-         (if version-suffix (cstr/lower-case version-suffix)))))
+         (when version-suffix (cstr/lower-case version-suffix)))))
 
 (defn is-primary-chromosome?
   [s]