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Sam record pair identification depends on required SAM fields #994

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Sam record pair identification depends on required SAM fields #994

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ba91430
feat: Pair identification of two sam records
DenisVerkhoturov Sep 21, 2017
272634a
feat: Pair identification tested
DenisVerkhoturov Sep 21, 2017
7843453
refactor: Pair identification test moved to SAMRecordUnitTest
DenisVerkhoturov Sep 21, 2017
3c01a88
fix: Add QNAME in pair identification
DenisVerkhoturov Sep 22, 2017
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14 changes: 14 additions & 0 deletions src/main/java/htsjdk/samtools/SAMRecord.java
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Original file line number Diff line number Diff line change
Expand Up @@ -333,6 +333,20 @@ private boolean hasReferenceName() {
return hasReferenceName(mReferenceIndex, mReferenceName);
}

/**
* @return {@code true} if records belong to the same pairwise alignment
*/
public boolean isPair(final SAMRecord record) {
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I'm confused about this function, a mate is another record with the same query name...why are you checking everything else, and not the QNAME? I'm sure there's a reason, but it should be explained in the javadoc as it is not obvious at all!

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Thank you for the remark, I think it does matter in SamRecord and I fixed it, but if we implement it in HitsForInsert it doesn't matter because it deals records with the same QNAME only. Here is the logic that produces HitsForInsert.

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I would suggest to move this to SamPairUtil, because there are already a lot of methods in SAMRecord that may be better to be used within an utility class. Eventually, reads would be accessed by an interface (e.g., #985) and thus this methods may live in an utility class that is implementation-independent.

return record != null
&& Objects.equals(this.getReadName(), record.getReadName())
&& this.getMateAlignmentStart() == record.getAlignmentStart()
&& record.getMateAlignmentStart() == this.getAlignmentStart()
&& !NO_ALIGNMENT_REFERENCE_NAME.equals(this.getMateReferenceName())
&& !NO_ALIGNMENT_REFERENCE_NAME.equals(record.getMateReferenceName())
&& Objects.equals(this.getReferenceName(), record.getMateReferenceName())
&& Objects.equals(record.getReferenceName(), this.getMateReferenceName());
}

/**
* @return true if this SAMRecord has a mate reference, either as a String or index (or both).
*/
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49 changes: 49 additions & 0 deletions src/test/java/htsjdk/samtools/SAMRecordUnitTest.java
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Expand Up @@ -1102,4 +1102,53 @@ private Object[][] hasAttributeTestData() throws IOException {
public void testHasAttribute(final SAMRecord samRecord, final String tag, final boolean expectedHasAttribute) {
Assert.assertEquals(samRecord.hasAttribute(tag), expectedHasAttribute);
}

@Test
public void testRecordsArePairIfTheyLinkEachOtherInMateFields() {
final SAMRecord first = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
first.setAlignmentStart(42);
first.setReferenceName("chrm1");
final SAMRecord second = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
second.setAlignmentStart(142);
second.setReferenceName("chrm2");

first.setMateAlignmentStart(second.getAlignmentStart());
first.setMateReferenceName(second.getReferenceName());
second.setMateAlignmentStart(first.getAlignmentStart());
second.setMateReferenceName(first.getReferenceName());

Assert.assertTrue(first.isPair(second));
Assert.assertTrue(second.isPair(first));
}

@Test
public void testRecordsArePairIfTheyHaveNoMateFields() {
final SAMRecord first = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
first.setReadName("example1");
first.setAlignmentStart(42);
first.setReferenceName("chrm1");
final SAMRecord second = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
first.setReadName("example1");
second.setAlignmentStart(142);
second.setReferenceName("chrm2");

Assert.assertFalse(first.isPair(second));
Assert.assertFalse(second.isPair(first));
}

@Test
public void testRecordsArePairIdentificationDoesNotThrowNpe() {
final SAMRecord first = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));

Assert.assertFalse(first.isPair(null));
}

@Test
public void testRecordsArePairIdentificationDoesNotThrowNpeIfFieldsAreUndefined() {
final SAMRecord first = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));
final SAMRecord second = new SAMRecord(new SAMFileHeader(new SAMSequenceDictionary()));

Assert.assertFalse(first.isPair(second));
Assert.assertFalse(second.isPair(first));
}
}