Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@364 348d0f76-0448-11de-a6fe-93d51630548a

build.xml

@@ -197,7 +197,7 @@
     <target name="test" depends="test.compile" description="Run unit tests">
         <mkdir dir="${report}"/>
         <echo message="Sting: Running test cases!"/>
-        <junit printsummary="yes" clonevm="yes" haltonfailure="yes">
+        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes">
             <formatter type="plain"/>
 
             <classpath>

java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java

@@ -0,0 +1,118 @@
+package org.broadinstitute.sting.utils;
+
+import org.junit.Test;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.After;
+
+import java.io.File;
+
+import edu.mit.broad.picard.reference.ReferenceSequence;
+import net.sf.samtools.util.StringUtil;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: mhanna
+ * Date: Apr 11, 2009
+ * Time: 2:32:52 PM
+ */
+public class FastaSequenceFile2Test {
+
+    private final String sequenceFileName = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
+    private FastaSequenceFile2 sequenceFile = null;
+
+    private final String firstBasesOfChrM = "GATCACAGGTCTATCACCCT";
+    private final String firstBasesOfChr1 = "taaccctaaccctaacccta";
+    private final String firstBasesOfChr8 = "GCAATTATGACACAAAAAAT";
+
+    @Before
+    public void doForEachTest() {
+        sequenceFile = new FastaSequenceFile2( new File(sequenceFileName) );
+    }
+
+    /**
+     * Tears down the test fixture after each call.
+     * <p/>
+     * Called after every test case method.
+     */
+    @After
+    public void undoForEachTest() {
+        sequenceFile = null;
+    }
+
+
+    @Test
+    public void testOpenFile() {
+        Assert.assertNotNull( sequenceFile );
+    }
+
+    @Test
+    public void testFirstSequence() {
+        ReferenceSequence sequence = sequenceFile.nextSequence();
+        Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chrM");
+        Assert.assertEquals( "First n bases of chrM are incorrect",
+                             StringUtil.bytesToString( sequence.getBases(), 0, firstBasesOfChrM.length() ),
+                             firstBasesOfChrM );
+    }
+
+    @Test
+    public void testNextSequence() {
+        ReferenceSequence sequence = null;
+
+        // Advance to chrM.
+        sequence = sequenceFile.nextSequence();
+        sequence = sequenceFile.nextSequence();
+
+        Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr1");
+
+        // Workaround: bytesToString for chr1 of the fasta file we've picked doesn't appear to work.
+        // TODO: Report this as sam-jdk bug.
+        byte[] firstOfChr1 = StringUtil.stringToBytes(firstBasesOfChr1);
+        byte[] firstOfSequence = new byte[firstBasesOfChr1.length()];
+        System.arraycopy(sequence.getBases(), 0, firstOfSequence, 0, firstOfSequence.length );
+
+        Assert.assertArrayEquals("First bases of chr1 are not correct", firstOfChr1, firstOfSequence );
+    }
+
+    @Test
+    public void testSeekToSequence() {
+        boolean success = sequenceFile.seekToContig("chr8");
+        Assert.assertTrue("Seek to seq chr8 failed", success );
+
+        ReferenceSequence sequence = sequenceFile.nextSequence();
+        Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr8");
+        Assert.assertEquals( "First n bases of chrc are incorrect",
+                             StringUtil.bytesToString( sequence.getBases(), 0, firstBasesOfChr8.length() ),
+                             firstBasesOfChr8 );
+    }
+
+    // TODO: Is NullPointerException *really* the right exception when a sequence is missing?
+    @Test(expected=NullPointerException.class)
+    public void testSeekToMissingSequence() {
+        boolean success = sequenceFile.seekToContig("absent");
+    }
+
+    @Test
+    public void testSeekBackward() {
+        boolean success = sequenceFile.seekToContig("chr9");
+        Assert.assertTrue("Unable to seek to contig 'chr9'", success);
+
+        success = sequenceFile.seekToContig("chr8",true);
+        Assert.assertTrue("Unable to seek backward to contig 'chr8'", success);
+
+        ReferenceSequence sequence = sequenceFile.nextSequence();
+        Assert.assertEquals("First sequence contig is not correct", sequence.getName(), "chr8");
+        Assert.assertEquals( "First n bases of chrc are incorrect",
+                             StringUtil.bytesToString( sequence.getBases(), 0, firstBasesOfChr8.length() ),
+                             firstBasesOfChr8 );        
+    }
+
+    @Test
+    public void testInvalidSeekBackward() {
+        boolean success = sequenceFile.seekToContig("chr9");
+        Assert.assertTrue("Unable to seek to contig 'chr9'", success);
+
+        success = sequenceFile.seekToContig("chr8");
+        Assert.assertFalse("Unable to seek backward to contig 'chr8'", success);
+    }
+}