Update CRAM reference test to include a genbank (gbk) referece with c…

…hromosome aliasing
igvteam · Sep 20, 2024 · 4448888 · 4448888
1 parent 068e20a
commit 4448888
Showing 1 changed file with 25 additions and 29 deletions.
diff --git a/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java b/src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java
@@ -30,9 +30,7 @@
 import org.junit.Before;
 import org.junit.Test;
 
-import java.io.IOException;
 import java.nio.charset.StandardCharsets;
-import java.util.Arrays;
 
 import static junit.framework.Assert.assertEquals;
 import static junit.framework.Assert.assertTrue;
@@ -43,53 +41,51 @@
 
 public class IGVReferenceSourceTest {
 
-    public static final String FASTA_URL = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa";
-    public static final String COMPRESSED_FASTA_URL = "https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.gz";
+    public static final String FASTA_URL = "https://igv.org/genomes/data/hg38/hg38.fa";
     public static final String EXPECTED_REFERENCE_BASES = "AAACCCAGGGCAAAGAATCTGGCCCTA"; //bases at 22:27198875-271988902
+    public static final String GBK_URL = "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/NC_012920.1.gbk";
+    public static final String GBK_EXPECTED_BASES = "tcatttctctaacagcagtaatattaataattttcatgat";
 
     @Before
     public void setUp() throws Exception {
 
     }
 
-    private void assertReferenceReqionRequestsWork(final String fastaUrl) throws IOException {
-        GenomeManager.getInstance().loadGenome(fastaUrl);
-
+    @Test
+    public void testGetReferenceBasesByRegion() throws Exception {
+        GenomeManager.getInstance().loadGenome(IGVReferenceSourceTest.FASTA_URL);
         IGVReferenceSource refSource = new IGVReferenceSource();
         String expected = EXPECTED_REFERENCE_BASES;
-        SAMSequenceRecord rec = new SAMSequenceRecord("22", 50818468);
+        SAMSequenceRecord rec = new SAMSequenceRecord("chr22", 50818468);
         byte[] bases = refSource.getReferenceBasesByRegion(rec, 27198874, expected.length());
         assertEquals(expected.length(), bases.length);
         assertEquals(expected, new String(bases, StandardCharsets.US_ASCII));
-    }
-
-    @Test
-    public void testGetReferenceBasesByRegion() throws Exception {
-        assertReferenceReqionRequestsWork(IGVReferenceSourceTest.FASTA_URL);
-    }
 
-    @Test
-    public void testGetReferenceBasesByRegionCompressed() throws Exception {
-        assertReferenceReqionRequestsWork(COMPRESSED_FASTA_URL);
+        // Test with a chr alias
+        rec = new SAMSequenceRecord("22", 50818468);
+        bases = refSource.getReferenceBasesByRegion(rec, 27198874, expected.length());
+        assertEquals(expected.length(), bases.length);
+        assertEquals(expected, new String(bases, StandardCharsets.US_ASCII));
     }
 
     @Test
-    public void testGetReferenceBasesCompressed() throws Exception {
-
-        GenomeManager.getInstance().loadGenome(COMPRESSED_FASTA_URL);
-
+    public void testGenbankReference() throws Exception {
+        GenomeManager.getInstance().loadGenome(GBK_URL);
+        String expected = GBK_EXPECTED_BASES.toUpperCase(); // Seq at NC_012920:7,279-7,318
         IGVReferenceSource refSource = new IGVReferenceSource();
-        SAMSequenceRecord rec = new SAMSequenceRecord("22", 50818468);
-        byte[] bases = refSource.getReferenceBases(rec, false);
-
-        assertEquals(50818468, bases.length);
+        SAMSequenceRecord rec = new SAMSequenceRecord("NC_012920", 16569);
+        byte[] bases = refSource.getReferenceBasesByRegion(rec, 7278, expected.length());
+        assertEquals(expected.length(), bases.length);
+        assertEquals(expected, new String(bases, StandardCharsets.US_ASCII));
 
-        assertEquals('N', bases[0]);
-        String expected = EXPECTED_REFERENCE_BASES;
-        String actual = new String(Arrays.copyOfRange(bases, 27198874, 27198874 + expected.length()), StandardCharsets.US_ASCII);
-        assertEquals(expected, actual);
+        // Test with a chr alias
+        rec = new SAMSequenceRecord("MT", 16569);
+        bases = refSource.getReferenceBasesByRegion(rec, 7278, expected.length());
+        assertEquals(expected.length(), bases.length);
+        assertEquals(expected, new String(bases, StandardCharsets.US_ASCII));
     }
 
+
 //    @Test
 //    public void testCompressedTiming() throws Exception {
 //