check reference sequence dictionary in header when comparing

Author: MatthewMah

src/main/java/adnascreen/AlignmentComparison.java

@@ -220,6 +220,10 @@ public static boolean compareAlignmentFiles(String finalOutputFilename, String[]
 				}
 				inputIterators[n] = inputReaders[n].iterator();
 				currentInputRecords[n] = inputIterators[n].next();
+				// check that reference is the same
+				if (!inputReaders[n].getFileHeader().getSequenceDictionary().equals(outputReader.getFileHeader().getSequenceDictionary())) {
+					return false;
+				}
 			}
 
 			// each final output file record should appear in exactly one input file

src/test/java/adnascreen/AlignmentComparisonTests.java

@@ -251,4 +251,26 @@ public void testNoCheckFail() {
 
 		assertThrows(org.apache.commons.cli.MissingOptionException.class, () -> AlignmentComparison.main(commandArray));
 	}
+	
+	@Test
+	public void testDifferentReferenceDictionary() {
+		ClassLoader classLoader = getClass().getClassLoader();
+		String samFilename1 = classLoader.getResource("alignment_comparison/multi_lib45.sam").getPath();
+		String samFilename2 = classLoader.getResource("alignment_comparison/multi_lib45_extraSeqDict.sam").getPath();
+		
+		String[] inputs = new String[1];
+		inputs[0] = samFilename2;
+		try {
+			assertFalse(AlignmentComparison.compareAlignmentFiles(samFilename1, inputs, tags, null));
+		} catch (IOException e) {
+			fail(e.getMessage());
+		}
+	}
+	
+	@Test
+	public void testDifferentReferenceDictionaryCommandLine() throws IOException, ParseException {
+		String samFilename1 = "alignment_comparison/multi_lib45.sam";
+		String samFilename2 = "alignment_comparison/multi_lib45_extraSeqDict.sam";
+		differentSAMCommandLine(samFilename1, samFilename2);
+	}
 }

src/test/resources/alignment_comparison/multi_lib45_extraSeqDict.sam

@@ -0,0 +1,12 @@
+@HD	VN:1.5	GO:none	SO:coordinate
+@SQ	SN:MT	LN:16569
+@SQ	SN:EXTRA	LN:10000
+@RG	ID:rg1	DT:2018-09-12T00:00:00-0400	LB:Lib1	PL:ILLUMINA	PM:NS500217 592	PU:HCG37BGX7.1	SM:I12561
+@RG	ID:rg2	DT:2018-09-12T00:00:00-0400	LB:Lib2	PL:ILLUMINA	PM:NS500217 592	PU:HCG37BGX7.2	SM:I12561
+@RG	ID:rg3	DT:2018-09-12T00:00:00-0400	LB:Lib3	PL:ILLUMINA	PM:NS500217 592	PU:HCG37BGX7.3	SM:I12561
+@RG	ID:rg4	DT:2018-09-27T00:00:00-0400	LB:Lib4	PL:ILLUMINA	PM:NS500217 598	PU:HYCVFBGX5.4	SM:I12561
+@RG	ID:rg5	DT:2018-09-27T00:00:00-0400	LB:Lib1	PL:ILLUMINA	PM:NS500217 598	PU:HYCVFBGX5.1	SM:I12561
+13602:9926:18684	0	MT	32	37	40M	*	0	0	ACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGA	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	X0:i:1	X1:i:0	MD:Z:39G0	XD:Z:AAGCATC_ATTGGCA_40	RG:Z:rg4	XG:i:0	NM:i:1	XM:i:1	XO:i:0	XT:A:U
+23605:7072:4424	1024	MT	119	37	57M	*	0	0	TCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCA	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	X0:i:1	X1:i:0	MD:Z:27C5C23	XD:Z:CCTGCAG_GCCAATG_57	RG:Z:rg4	XG:i:0	NM:i:2	XM:i:2	XO:i:0	XT:A:U
+12304:12820:10743	0	MT	324	37	36M	*	0	0	CCACAGCACTTAAACACATCTCTGCCAAACCCCAAA	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	X0:i:1	X1:i:0	MD:Z:36	XD:Z:CCTGCAG_TGGCCAT_36	RG:Z:rg5	XG:i:0	NM:i:0	XM:i:0	XO:i:0	XT:A:U
+22412:14443:18175	0	MT	325	37	45M	*	0	0	CACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAAC	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE	X0:i:1	X1:i:0	MD:Z:45	XD:Z:GGATGCT_CAATTGC_45	RG:Z:rg5	XG:i:0	NM:i:0	XM:i:0	XO:i:0	XT:A:U