Use XZ for LZMA compression in CRAM

chrovis · Aug 27, 2024 · 421df41 · 421df41
1 parent b0b8cb4
commit 421df41
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/src/cljam/io/cram/decode/structure.clj b/src/cljam/io/cram/decode/structure.clj
@@ -115,7 +115,7 @@
                 compressor (case method
                              1 CompressorStreamFactory/GZIP
                              2 CompressorStreamFactory/BZIP2
-                             3 CompressorStreamFactory/LZMA
+                             3 CompressorStreamFactory/XZ
                              (throw
                               (ex-info (str "compression method " method
                                             " not supported")

diff --git a/src/cljam/io/cram/encode/compressor.clj b/src/cljam/io/cram/encode/compressor.clj
@@ -2,7 +2,7 @@
   (:import [java.io ByteArrayOutputStream OutputStream]
            [org.apache.commons.compress.compressors.bzip2 BZip2CompressorOutputStream]
            [org.apache.commons.compress.compressors.gzip GzipCompressorOutputStream]
-           [org.apache.commons.compress.compressors.lzma LZMACompressorOutputStream]
+           [org.apache.commons.compress.compressors.xz XZCompressorOutputStream]
            [org.apache.commons.io.output CountingOutputStream]))
 
 (defprotocol ICompressor
@@ -32,7 +32,7 @@
     {:compressor :bzip, :data (.toByteArray baos)}))
 
 (deftype LZMACompressor
-         [^LZMACompressorOutputStream out ^ByteArrayOutputStream baos]
+         [^XZCompressorOutputStream out ^ByteArrayOutputStream baos]
   ICompressor
   (compressor-output-stream [_] out)
   (->compressed-result [_]
@@ -60,7 +60,7 @@
                                                           uncompressed)
                                      :bzip (compress-with #(BZip2CompressorOutputStream. %)
                                                           uncompressed)
-                                     :lzma (compress-with #(LZMACompressorOutputStream. %)
+                                     :lzma (compress-with #(XZCompressorOutputStream. %)
                                                           uncompressed)
                                      (throw
                                       (ex-info (str "compression method " method
@@ -78,7 +78,7 @@
                 :raw (->RawCompressor baos)
                 :gzip (->GzipCompressor (GzipCompressorOutputStream. baos) baos)
                 :bzip (->BZip2Compressor (BZip2CompressorOutputStream. baos) baos)
-                :lzma (->LZMACompressor (LZMACompressorOutputStream. baos) baos)
+                :lzma (->LZMACompressor (XZCompressorOutputStream. baos) baos)
                 :best (->SelectiveCompressor baos #{:raw :gzip :bzip :lzma})
                 (if (set? method-or-methods)
                   (->SelectiveCompressor baos method-or-methods)

diff --git a/test/cljam/io/cram/data_series_test.clj b/test/cljam/io/cram/data_series_test.clj
@@ -10,7 +10,7 @@
   (:import [java.io ByteArrayInputStream ByteArrayOutputStream]
            [org.apache.commons.compress.compressors.bzip2 BZip2CompressorInputStream]
            [org.apache.commons.compress.compressors.gzip GzipCompressorInputStream]
-           [org.apache.commons.compress.compressors.lzma LZMACompressorInputStream]))
+           [org.apache.commons.compress.compressors.xz XZCompressorInputStream]))
 
 (deftest build-data-series-decoders-test
   (let [encodings {:BA {:codec :external, :content-id 1}
@@ -454,7 +454,7 @@
                      :raw bais
                      :gzip (GzipCompressorInputStream. bais)
                      :bzip (BZip2CompressorInputStream. bais)
-                     :lzma (LZMACompressorInputStream. bais))]
+                     :lzma (XZCompressorInputStream. bais))]
       (lsb/read-bytes in raw-size))))
 
 (deftest build-data-series-encoders-test