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Zero len array #1674

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merged 3 commits into from
Aug 3, 2023
Merged

Zero len array #1674

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1cc8a2c
Remove setUnsignedArrayAttribute zero-length-array check
jmarshall Jun 13, 2023
f2f92d4
Remove Slice setAttribute zero-length-array check
jmarshall Jun 13, 2023
c9ad747
removed unused setAttribute methods
gileshall Aug 1, 2023
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3 changes: 0 additions & 3 deletions src/main/java/htsjdk/samtools/SAMRecord.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
}

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35 changes: 0 additions & 35 deletions src/main/java/htsjdk/samtools/cram/structure/Slice.java
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Expand Up @@ -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.
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13 changes: 13 additions & 0 deletions src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
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Expand Up @@ -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},
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