Java Code Examples for htsjdk.samtools.SAMRecord#getContig()

@Test
// One intergenic read (no other gene models overlapping)
public void testIntergeicRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 200, 210, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, true, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector);

	Assert.assertEquals(r.getStringAttribute("GE"), null);
	Assert.assertEquals(r.getStringAttribute("GS"), null);
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTERGENIC.name());
}
 

@Test
// 	One UTR read (wrong strand, no other gene models overlapping)
public void testUTRReadWrongStrand () {
	SAMRecord r = getFakeRecord(testBAMFile, 91, 95, true);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector);

	String GE=r.getStringAttribute("GE");
	String GS=r.getStringAttribute("GS");
	String XF = r.getStringAttribute("XF");

	Assert.assertNull(GE);
	Assert.assertNull(GS);
	Assert.assertEquals(XF, LocusFunction.INTERGENIC.name());
}
 

@Test
// One intergenic read (no other gene models overlapping)
public void testIntergeicRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 200, 210, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, true, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), null);
	Assert.assertEquals(r.getStringAttribute("gs"), null);
	Assert.assertEquals(r.getStringAttribute("gf"), null);
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTERGENIC.name());
}
 

@Test
// 	2) One intronic read (no other gene models overlapping)
public void testIntronicRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 50, 75, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.INTRONIC.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTRONIC.name());
}
 

@Test
// 	One UTR read (correct strand, no other gene models overlapping)
public void testUTRRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 91, 95, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.UTR.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.UTR.name());
}
 

@Test
// 	One UTR read (wrong strand, no other gene models overlapping)
public void testUTRReadWrongStrand () {
	SAMRecord r = getFakeRecord(testBAMFile, 91, 95, true);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.UTR.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTERGENIC.name());
}
 

@Test
// One CODING read (correct strand, no other gene models overlapping)
public void testCodingRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 2, 8, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.CODING.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

@Test
// One CODING read (wrong strand, no other gene models overlapping)
public void testCodingReadWrongStrand () {
	SAMRecord r = getFakeRecord(testBAMFile, 2, 8, true);
	boolean negStrandFlag = r.getReadNegativeStrandFlag();
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.CODING.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTERGENIC.name());
}
 

@Test
// 	2) One intronic read (no other gene models overlapping)
public void testIntronicRead () {
	SAMRecord r = getFakeRecord(testBAMFile, 50, 75, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector);

	String geneName = r.getStringAttribute("GE");
	String geneStrand = r.getStringAttribute("GS");
	String XF = r.getStringAttribute("XF");

	Assert.assertNull(geneName);
	Assert.assertNull(geneStrand);

	Assert.assertEquals(XF, LocusFunction.INTRONIC.name());
}
 

@Test(enabled=true)
// a read with 2 alignment blocks that both overlap a single gene, both in an exon.
public void testSplitReadExonExonSameGene () {
	SAMRecord r = getFakeSplitRecord(testBAMFile, 91, 100, 151,160, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 200, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 200, 1, 200, 3, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	tx.addExon(150, 160);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector);
	Assert.assertEquals(r.getStringAttribute("GE"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("GS"), "+");
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

@Test
public void testIntergenicCorrectIntronicWrong () {
	SAMRecord r = getFakeRecord(testBAMFile, 50, 60, false);
	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, true, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);
	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	r=tagger.setAnnotations(r, geneOverlapDetector, false);

	String gn = r.getStringAttribute("gn");
	String gs = r.getStringAttribute("gs");
	String gf = r.getStringAttribute("gf");

	Assert.assertEquals(gn, gene.getName());
	Assert.assertEquals(gs, "-");
	Assert.assertEquals(gf, LocusFunction.INTRONIC.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTERGENIC.name());
}
 

@Test(enabled=true)
// a read with 2 alignment blocks that both overlap a single gene, once in an intron and once an exon.
public void testSplitReadExonicIntronicSameGene () {
	SAMRecord r = getFakeSplitRecord(testBAMFile, 91, 100, 131,140, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 200, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 200, 1, 200, 3, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	tx.addExon(150, 160);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName()+","+gene.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+,+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.CODING.name() + "," + LocusFunction.INTRONIC.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

@Test(enabled=true)
// a read with 2 alignment blocks that both overlap a single gene, once in an intron and once an exon.
public void testSplitReadExonicIntronicSameGene () {
	SAMRecord r = getFakeSplitRecord(testBAMFile, 91, 100, 131,140, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 200, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 200, 1, 200, 3, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	tx.addExon(150, 160);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector);
	Assert.assertEquals(r.getStringAttribute("GE"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("GS"), "+");
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

@Test
public void testIntronicCorrectCodingWrong () {
	// read on the negative strand
	SAMRecord r = getFakeRecord(testBAMFile, 91, 100, true);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 100, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	// gene with 2 exons, 1 coding from 50-60, 1 coding from 150-160. Negative strand gene.
	GeneFromGTF gene2 = new GeneFromGTF(r.getContig(), 50, 160, true, "B", "coding", "B", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx2 = gene2.addTranscript("trans2", 50, 160, 50, 150, 2, "trans2", "trans2", "coding");
	tx2.addExon(50, 60);
	tx2.addExon(150, 160);
	geneOverlapDetector.addLhs(gene2, gene2);

	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector, false);
	String gn = r.getStringAttribute("gn");
	String gs = r.getStringAttribute("gs");
	String gf = r.getStringAttribute("gf");

	// names always come out alphabetically sorted.
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName()+","+gene2.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+,-");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.CODING.name() + "," + LocusFunction.INTRONIC.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.INTRONIC.name());
}
 

@Test
public void testSplitReadExonicIntronicDifferentGenes() {
	SAMRecord r = getFakeSplitRecord(testBAMFile, 1, 10, 91,100, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 100, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	// gene with 2 exons, 1 coding from 50-60, 1 coding from 150-160. Positive strand gene.
	GeneFromGTF gene2 = new GeneFromGTF(r.getContig(), 50, 160, false, "B", "coding", "B", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx2 = gene2.addTranscript("trans2", 50, 160, 50, 150, 2, "trans2", "trans2", "coding");
	tx2.addExon(50, 60);
	tx2.addExon(150, 160);
	geneOverlapDetector.addLhs(gene2, gene2);

	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector);
	Assert.assertEquals(r.getStringAttribute("GE"), gene.getName());
	Assert.assertEquals(r.getStringAttribute("GS"), "+");
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());

}
 

@Test
// Read overlaps exon on one gene, and intron on another, all on the same strand.
public void testCodingAndIntronic () {
	// read on the positive strand
	SAMRecord r = getFakeRecord(testBAMFile, 91, 100, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 100, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	// gene with 2 exons, 1 coding from 50-60, 1 coding from 150-160. Negative strand gene.
	GeneFromGTF gene2 = new GeneFromGTF(r.getContig(), 50, 160, false, "B", "coding", "B", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx2 = gene2.addTranscript("trans2", 50, 160, 50, 150, 2, "trans2", "trans2", "coding");
	tx2.addExon(50, 60);
	tx2.addExon(150, 160);
	geneOverlapDetector.addLhs(gene2, gene2);

	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector);

	String geneTagged = r.getStringAttribute("GE");
	String strandTagged = r.getStringAttribute("GS");

	// names always come out alphabetically sorted.
	Assert.assertEquals(geneTagged, gene.getName());
	Assert.assertEquals(strandTagged, "+");
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

@Test
// Read overlaps exon on one gene, and intron on another, all on the same strand.
public void testCodingAndIntronic () {
	// read on the negative strand
	SAMRecord r = getFakeRecord(testBAMFile, 91, 100, false);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 100, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	// gene with 2 exons, 1 coding from 50-60, 1 coding from 150-160. Negative strand gene.
	GeneFromGTF gene2 = new GeneFromGTF(r.getContig(), 50, 160, false, "B", "coding", "B", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx2 = gene2.addTranscript("trans2", 50, 160, 50, 150, 2, "trans2", "trans2", "coding");
	tx2.addExon(50, 60);
	tx2.addExon(150, 160);
	geneOverlapDetector.addLhs(gene2, gene2);

	TagReadWithGeneFunction tagger = new TagReadWithGeneFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector, false);

	// names always come out alphabetically sorted.
	Assert.assertEquals(r.getStringAttribute("gn"), gene.getName()+","+gene2.getName());
	Assert.assertEquals(r.getStringAttribute("gs"), "+,+");
	Assert.assertEquals(r.getStringAttribute("gf"), LocusFunction.CODING.name() + "," + LocusFunction.INTRONIC.name());
	Assert.assertEquals(r.getStringAttribute("XF"), LocusFunction.CODING.name());
}
 

private void writeReadReportLine(List<SAMRecord> r1List, List<SAMRecord> r2List, List<String> tagNames, PrintStream writer) {
	// only the 2nd read can be a multimapper.
	if (!validateReadSetSize(r1List, r2List)) return;
	
	SAMRecord r1 = r1List.get(0);
	
	String r1Contig=r1.getContig().replaceAll(this.TRIM_CONTIG_STRING, "");
	int r1Pos=r1.getAlignmentStart();
	
	for (SAMRecord r: r2List) {
		List<String> line = new ArrayList<>();
		Collections.addAll(line, r1.getReadName(), r1Contig, Integer.toString(r1Pos), Integer.toString(r1.getMappingQuality()));
		String r2Contig = r.getContig();
		if (r2Contig!=null) r2Contig.replaceAll(this.TRIM_CONTIG_STRING, "");
		if (r2Contig==null) r2Contig="NA";
		int r2Pos=r.getAlignmentStart();
		// if the contig and position are the same, don't emit the read
		if (r1Contig.equals(r2Contig) && r1Pos==r2Pos) 
			continue;
		
		Collections.addAll(line, r2Contig, Integer.toString(r2Pos), Integer.toString(r.getMappingQuality()), Boolean.toString(!r.isSecondaryAlignment()));
		for (String tagName: tagNames) {
			line.add(getTagValueAsString(r1, tagName));
			line.add(getTagValueAsString(r, tagName));
		}
		writer.println(StringUtils.join(line, "\t"));
	}		
}
 

@Test
public void testIntronicCorrectUTRWrong () {
	// read on the negative strand
	SAMRecord r = getFakeRecord(testBAMFile, 91, 100, true);

	// gene with 2 exons, 1 coding from 1-10, one UTR from 91-100.  Positive strand gene.
	GeneFromGTF gene = new GeneFromGTF(r.getContig(), 1, 100, false, "A", "coding", "A", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx = gene.addTranscript("trans1", 1, 100, 1, 90, 2, "trans1", "trans1", "coding");
	tx.addExon(1, 10);
	tx.addExon(91, 100);
	OverlapDetector<Gene> geneOverlapDetector = new OverlapDetector<>(0, 0);
	geneOverlapDetector.addLhs(gene, gene);

	// gene with 2 exons, 1 coding from 50-60, 1 coding from 150-160. Negative strand gene.
	GeneFromGTF gene2 = new GeneFromGTF(r.getContig(), 50, 160, true, "B", "coding", "B", "coding", 1);
	final GeneFromGTF.TranscriptFromGTF tx2 = gene2.addTranscript("trans2", 50, 160, 50, 150, 2, "trans2", "trans2", "coding");
	tx2.addExon(50, 60);
	tx2.addExon(150, 160);
	geneOverlapDetector.addLhs(gene2, gene2);

	TagReadWithGeneExonFunction tagger = new TagReadWithGeneExonFunction();
	List <Gene> genes = new ArrayList <> (geneOverlapDetector.getAll());
	Collections.sort(genes, TagReadWithGeneFunction.GENE_NAME_COMPARATOR);

	r=tagger.setAnnotations(r, geneOverlapDetector);
	String GE = r.getStringAttribute("GE");
	String GS = r.getStringAttribute("GS");
	String XF = r.getStringAttribute("XF");

	// names always come out alphabetically sorted.
	Assert.assertNull(GE);
	Assert.assertNull(GS);

	Assert.assertEquals(XF, LocusFunction.INTRONIC.name());
}
 

private static void writeToSlice(@NotNull SAMFileWriter writer, @NotNull CloseableIterator<SAMRecord> iterator) {
    String contig = "";
    while (iterator.hasNext()) {
        SAMRecord record = iterator.next();
        if (record.getContig() != null && !contig.equals(record.getContig())) {
            contig = record.getContig();
            LOGGER.info("Reading contig: {}", contig);
        }
        writer.addAlignment(record);
    }
    iterator.close();
}