Replace lsb protocol invocations with fn counterparts

chrovis · Nov 14, 2023 · 3726b73 · 3726b73
1 parent 185af98
commit 3726b73
Show file tree

Hide file tree

Showing 12 changed files with 28 additions and 28 deletions.
diff --git a/src/cljam/algo/convert.clj b/src/cljam/algo/convert.clj
@@ -1,19 +1,19 @@
 (ns cljam.algo.convert
   "Converters between equivalent formats: SAM/BAM and FASTA/TwoBit."
-  (:require [clojure.tools.logging :as logging]
-            [clojure.string :as cstr]
-            [cljam.common :refer [*n-threads* get-exec-n-threads]]
-            [cljam.io.sam :as sam]
+  (:require [cljam.common :refer [*n-threads* get-exec-n-threads]]
             [cljam.io.bam.encoder :as encoder]
+            [cljam.io.fastq :as fq]
+            [cljam.io.sam :as sam]
             [cljam.io.sam.util.flag :as flag]
             [cljam.io.sam.util.refs :as refs]
-            [cljam.util.sequence :as util-seq]
             [cljam.io.sequence :as cseq]
-            [cljam.io.fastq :as fq]
             [cljam.io.util :as io-util]
+            [cljam.util.sequence :as util-seq]
+            [clojure.string :as cstr]
+            [clojure.tools.logging :as logging]
             [com.climate.claypoole :as cp])
-  (:import [java.nio ByteBuffer]
-           [cljam.io.fastq FASTQRead]))
+  (:import [cljam.io.fastq FASTQRead]
+           [java.io ByteArrayOutputStream]))
 
 ;;; SAM <-> BAM
 
@@ -30,9 +30,9 @@
         n-threads (get-exec-n-threads)]
     (doseq [blocks (cp/pmap (if (= n-threads 1) :serial (dec n-threads))
                             (fn [chunk']
-                              (mapv #(let [bb (ByteBuffer/allocate (encoder/get-block-size %))]
-                                       (encoder/encode-alignment bb % refs)
-                                       {:data (.array bb)})
+                              (mapv #(let [baos (ByteArrayOutputStream. (encoder/get-block-size %))]
+                                       (encoder/encode-alignment baos % refs)
+                                       {:data (.toByteArray baos)})
                                     chunk'))
                             (partition-all num-block (sam/read-alignments rdr {})))]
       (sam/write-blocks wtr blocks))))

diff --git a/src/cljam/io/bam/core.clj b/src/cljam/io/bam/core.clj
@@ -6,7 +6,7 @@
              [writer :as writer]]
             [cljam.io.bam-index :as bai]
             [cljam.io.util.bgzf :as bgzf]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.data-io :as lsb]
             [cljam.util :as util])
   (:import java.util.Arrays
            [java.io DataInputStream DataOutputStream IOException FileNotFoundException]

diff --git a/src/cljam/io/bam/encoder.clj b/src/cljam/io/bam/encoder.clj
@@ -7,7 +7,7 @@
             [cljam.io.sam.util.quality :as qual]
             [cljam.io.sam.util.cigar :as cigar]
             [cljam.io.sam.util.sequence :as seq]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.bam.common :as common]))
 
 (def ^:private ^:const fixed-tag-size 3)

diff --git a/src/cljam/io/bam/reader.clj b/src/cljam/io/bam/reader.clj
@@ -5,7 +5,7 @@
             [cljam.io.sam.util.header :as header]
             [cljam.io.bam-index.core :as bai]
             [cljam.io.bam.decoder :as decoder]
-            [cljam.io.util.lsb :as lsb])
+            [cljam.io.util.lsb.data-io :as lsb])
   (:import [java.io Closeable FileNotFoundException]
            [cljam.io.bam.decoder BAMRawBlock]
            [bgzf4j BGZFInputStream]))

diff --git a/src/cljam/io/bam/writer.clj b/src/cljam/io/bam/writer.clj
@@ -4,7 +4,7 @@
             [cljam.io.protocols :as protocols]
             [cljam.io.sam.util.refs :as refs]
             [cljam.io.sam.util.header :as header]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.bam.common :as common]
             [cljam.io.bam.encoder :as encoder]
             [cljam.io.bam.decoder :as bam-decoder]

diff --git a/src/cljam/io/bam_index/reader.clj b/src/cljam/io/bam_index/reader.clj
@@ -1,6 +1,6 @@
 (ns cljam.io.bam-index.reader
   (:require [clojure.java.io :as cio]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.bam-index.common :refer [bai-magic]]
             [cljam.io.util.chunk :as chunk]
             [cljam.util :as util])

diff --git a/src/cljam/io/bam_index/writer.clj b/src/cljam/io/bam_index/writer.clj
@@ -2,7 +2,7 @@
   (:require [com.climate.claypoole :as cp]
             [cljam.common :refer [get-exec-n-threads]]
             [cljam.io.util.bgzf :as bgzf]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.util.bin :as util-bin]
             [cljam.io.bam-index.common :refer [linear-index-shift
                                                linear-index-depth

diff --git a/src/cljam/io/bcf/reader.clj b/src/cljam/io/bcf/reader.clj
@@ -4,7 +4,7 @@
             [cljam.io.protocols :as protocols]
             [cljam.io.util.bgzf :as bgzf]
             [cljam.io.util.byte-buffer :as bb]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.vcf.reader :as vcf-reader]
             [cljam.io.vcf.util :as vcf-util]
             [cljam.util :as util]

diff --git a/src/cljam/io/bcf/writer.clj b/src/cljam/io/bcf/writer.clj
@@ -2,7 +2,7 @@
   (:require [clojure.string :as cstr]
             [cljam.io.protocols :as protocols]
             [cljam.io.util.bgzf :as bgzf]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.vcf.writer :as vw]
             [cljam.io.vcf.util :as vcf-util]
             [cljam.util :as util])

diff --git a/src/cljam/io/bigwig.clj b/src/cljam/io/bigwig.clj
@@ -4,7 +4,7 @@
   specifications."
   (:require [clojure.java.io :as cio]
             [cljam.io.protocols :as protocols]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.data-io :as lsb]
             [cljam.util :as util])
   (:import [java.net URL]
            [java.io Closeable IOException RandomAccessFile]

diff --git a/src/cljam/io/csi.clj b/src/cljam/io/csi.clj
@@ -1,13 +1,13 @@
 (ns cljam.io.csi
   "Basic I/O of CSI:Coordinate Sorted Index files."
-  (:require [clojure.string :as cstr]
-            [cljam.io.util.bgzf :as bgzf]
-            [cljam.io.util.lsb :as lsb]
+  (:require [cljam.io.util.bgzf :as bgzf]
+            [cljam.io.util.bin :as util-bin]
             [cljam.io.util.chunk :as chunk]
-            [cljam.io.util.bin :as util-bin])
-  (:import java.util.Arrays
-           [java.io DataInputStream DataOutputStream IOException]
-           [java.nio ByteBuffer ByteOrder]))
+            [cljam.io.util.lsb.io-stream :as lsb]
+            [clojure.string :as cstr])
+  (:import [java.io DataInputStream DataOutputStream IOException]
+           [java.nio ByteBuffer ByteOrder]
+           java.util.Arrays))
 
 (def ^:const ^:private csi-magic "CSI\1")
 

diff --git a/src/cljam/io/tabix.clj b/src/cljam/io/tabix.clj
@@ -2,7 +2,7 @@
   "Alpha - subject to change.
   Reader of a TABIX format file."
   (:require [cljam.io.util.bgzf :as bgzf]
-            [cljam.io.util.lsb :as lsb]
+            [cljam.io.util.lsb.io-stream :as lsb]
             [cljam.io.util.bin :as util-bin]
             [clojure.string :as cstr])
   (:import java.util.Arrays