Zero len array (#1674)

* Remove setUnsignedArrayAttribute zero-length-array check This function was omitted from PR #1194. Zero-length 'B' arrays are valid, so remove this check too and add a test case. * Remove Slice setAttribute zero-length-array check Slices' optional tags follow the rules for BAM tagged fields, so zero-length 'B' arrays are valid. Slice tags are currently unused, so the question is somewhat moot and there are no test cases. * removed unused setAttribute methods --------- Co-authored-by: John Marshall <[email protected]>
samtools · Aug 3, 2023 · d486d53 · d486d53
1 parent 44817ee
commit d486d53
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Showing 3 changed files with 13 additions and 38 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java
@@ -1541,9 +1541,6 @@ public void setUnsignedArrayAttribute(final String tag, final Object value) {
         if (!value.getClass().isArray()) {
             throw new IllegalArgumentException("Non-array passed to setUnsignedArrayAttribute for tag " + tag);
         }
-        if (Array.getLength(value) == 0) {
-            throw new IllegalArgumentException("Empty array passed to setUnsignedArrayAttribute for tag " + tag);
-        }
         setAttribute(SAMTag.makeBinaryTag(tag), value, true);
     }
 

diff --git a/src/main/java/htsjdk/samtools/cram/structure/Slice.java b/src/main/java/htsjdk/samtools/cram/structure/Slice.java
@@ -735,41 +735,6 @@ public void setReferenceMD5(final CRAMReferenceRegion cramReferenceRegion) {
         }
     }
 
-    /**
-     * Hijacking attributes-related methods from SAMRecord:
-     */
-
-    /**
-     * Set a value for the tag.
-     * @param tag tag ID as a short integer as returned by {@link SAMTag#makeBinaryTag(String)}
-     * @param value tag value
-     */
-    public void setAttribute(final String tag, final Object value) {
-        if (value != null && value.getClass().isArray() && Array.getLength(value) == 0) {
-            throw new IllegalArgumentException("Empty value passed for tag " + tag);
-        }
-        setAttribute(SAMTag.makeBinaryTag(tag), value);
-    }
-
-    void setAttribute(final short tag, final Object value) {
-        setAttribute(tag, value, false);
-    }
-
-    void setAttribute(final short tag, final Object value, final boolean isUnsignedArray) {
-        if (value == null) {
-            if (this.sliceTags != null) this.sliceTags = this.sliceTags.remove(tag);
-        } else {
-            final SAMBinaryTagAndValue tmp;
-            if (!isUnsignedArray) {
-                tmp = new SAMBinaryTagAndValue(tag, value);
-            } else {
-                tmp = new SAMBinaryTagAndUnsignedArrayValue(tag, value);
-            }
-            if (this.sliceTags == null) this.sliceTags = tmp;
-            else this.sliceTags = this.sliceTags.insert(tmp);
-        }
-    }
-
     /**
      * Uses a Multiple Reference Slice Alignment Reader to determine the reference spans of a MULTI_REF Slice.
      * Used for creating CRAI/BAI index entries.

diff --git a/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java b/src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
@@ -1124,6 +1124,19 @@ public void test_setAttribute_empty_array() {
         Assert.assertNull(record.getStringAttribute(ARRAY_TAG));
     }
 
+    @Test
+    public void test_setUnsignedArrayAttribute_empty_array() {
+        final SAMFileHeader header = new SAMFileHeader();
+        final SAMRecord record = new SAMRecord(header);
+        Assert.assertNull(record.getStringAttribute(ARRAY_TAG));
+        record.setUnsignedArrayAttribute(ARRAY_TAG, new int[0]);
+        Assert.assertNotNull(record.getUnsignedIntArrayAttribute(ARRAY_TAG));
+        Assert.assertEquals(record.getUnsignedIntArrayAttribute(ARRAY_TAG), new int[0]);
+        Assert.assertEquals(record.getAttribute(ARRAY_TAG), new char[0]);
+        record.setAttribute(ARRAY_TAG, null);
+        Assert.assertNull(record.getStringAttribute(ARRAY_TAG));
+    }
+
     private static Object[][] getEmptyArrays() {
         return new Object[][]{
                 {new int[0], int[].class},