more consistent ExternalDataBlock

samtools · Dec 3, 2018 · f59abd0 · f59abd0
1 parent b3ff8ed
commit f59abd0
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Showing 4 changed files with 23 additions and 21 deletions.
diff --git a/src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java b/src/main/java/htsjdk/samtools/cram/build/ContainerFactory.java
@@ -176,7 +176,7 @@ private static Slice buildSlice(final List<CramCompressionRecord> records,
         for (final Integer key : map.keySet()) {
             final ExternalCompressor compressor = header.externalCompressors.get(key);
             final byte[] rawData = map.get(key).toByteArray();
-            final ExternalDataBlock externalBlock = new ExternalDataBlock(key, compressor, rawData);
+            final ExternalDataBlock externalBlock = Block.externalDataBlock(key, compressor, rawData);
             slice.external.put(key, externalBlock);
         }
 

diff --git a/src/main/java/htsjdk/samtools/cram/structure/block/Block.java b/src/main/java/htsjdk/samtools/cram/structure/block/Block.java
@@ -20,6 +20,7 @@
 import htsjdk.samtools.cram.CRAMException;
 import htsjdk.samtools.cram.common.CramVersions;
 import htsjdk.samtools.cram.compression.ExternalCompression;
+import htsjdk.samtools.cram.compression.ExternalCompressor;
 import htsjdk.samtools.cram.io.*;
 import htsjdk.samtools.util.RuntimeIOException;
 
@@ -115,7 +116,7 @@ public static SliceHeaderBlock uncompressedSliceHeaderBlock(final byte[] rawCont
     }
 
     /**
-     * Create a new core block with the given uncompressed content.
+     * Create a new core data block with the given uncompressed content.
      * The block will have RAW (no) compression and CORE content type.
      *
      * @param rawContent the uncompressed content of the block
@@ -125,6 +126,24 @@ public static CoreDataBlock uncompressedCoreBlock(final byte[] rawContent) {
         return new CoreDataBlock(BlockCompressionMethod.RAW, rawContent);
     }
 
+    /**
+     * Create a new external data block with the given content ID, compressor, and uncompressed content.
+     * The block will have EXTERNAL content type.
+     *
+     * @param contentId the external identifier for the block
+     * @param compressor which external compressor to use on this block
+     * @param rawContent the uncompressed content of the block
+     * @return a new {@link ExternalDataBlock} object
+     */
+    public static ExternalDataBlock externalDataBlock(final int contentId, final ExternalCompressor compressor, final byte[] rawContent) {
+        // remove after https://github.com/samtools/htsjdk/issues/1232
+        if (contentId == Block.NO_CONTENT_ID) {
+            throw new CRAMException("Valid Content ID required.  Given: " + contentId);
+        }
+
+        return new ExternalDataBlock(compressor.getMethod(), compressor.compress(rawContent), contentId);
+    }
+
     public final BlockCompressionMethod getMethod() {
         return method;
     }

diff --git a/src/main/java/htsjdk/samtools/cram/structure/block/ExternalDataBlock.java b/src/main/java/htsjdk/samtools/cram/structure/block/ExternalDataBlock.java
@@ -24,23 +24,6 @@ public class ExternalDataBlock extends Block {
         this.contentId = contentId;
     }
 
-    /**
-     * Create a new external data block with the given content ID, compressor, and uncompressed content.
-     * The block will have EXTERNAL content type.
-     *
-     * @param contentId the external identifier for the block
-     * @param compressor which external compressor to use on this block
-     * @param rawContent the uncompressed content of the block
-     */
-    public ExternalDataBlock(final int contentId, final ExternalCompressor compressor, final byte[] rawContent) {
-        this(compressor.getMethod(), compressor.compress(rawContent), contentId);
-
-        // remove after https://github.com/samtools/htsjdk/issues/1232
-        if (contentId == Block.NO_CONTENT_ID) {
-            throw new CRAMException("Valid Content ID required.  Given: " + contentId);
-        }
-    }
-
     @Override
     public final int getContentId() {
         return contentId;

diff --git a/src/test/java/htsjdk/samtools/cram/structure/BlockTest.java b/src/test/java/htsjdk/samtools/cram/structure/BlockTest.java
@@ -110,7 +110,7 @@ public void testExternalBlockRoundTrips() {
         final byte[] uncompressedData = "A TEST STRING WITH REDUNDANCY AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA".getBytes();
         final byte[] compressedData = compressor.compress(uncompressedData);
 
-        final Block extBlock = new ExternalDataBlock(contentID, compressor, uncompressedData);
+        final Block extBlock = Block.externalDataBlock(contentID, compressor, uncompressedData);
 
         final Block rtBlock2 = roundTrip(extBlock, CramVersions.CRAM_v2_1);
         contentCheck(rtBlock2, uncompressedData, compressedData);
@@ -140,6 +140,6 @@ public void testExternalBlockContentId() {
 
         // not allowed for external
         final int contentID = Block.NO_CONTENT_ID;
-        new ExternalDataBlock(contentID, compressor, uncompressedData);
+        Block.externalDataBlock(contentID, compressor, uncompressedData);
     }
 }