UnitTests for ConsensusSpan infrastructure
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5929 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
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import com.google.java.contract.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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/*
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@ -28,12 +29,14 @@ import org.broadinstitute.sting.utils.GenomeLoc;
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*/
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/**
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* Created by IntelliJ IDEA.
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* User: depristo
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* Date: 4/8/11
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* Time: 3:01 PM
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* To change this template use File | Settings | File Templates.
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*/
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* Created by IntelliJ IDEA.
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* User: depristo
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* Date: 4/8/11
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* Time: 3:01 PM
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*
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* Represents a span of a consensus region (conserved, or variable) on the reference genome. Supports
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* either absolute or relative (refStart) positioning of the span.
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*/
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final class ConsensusSpan {
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/**
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@ -58,7 +61,13 @@ final class ConsensusSpan {
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final GenomeLoc loc;
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final Type consensusType;
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@Requires({"refStart >= 0", "loc != null", "consensusType != null"})
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@Ensures({"this.refStart == refStart", "this.loc.equals(loc)", "this.consensusType.equals(consensusType)"})
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public ConsensusSpan(final int refStart, GenomeLoc loc, ConsensusSpan.Type consensusType) {
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if ( refStart < 0 ) throw new RuntimeException("RefStart must be greater than 0: " + refStart);
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if ( loc == null ) throw new RuntimeException("Loc must not be null");
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if ( consensusType == null ) throw new RuntimeException("ConsensusType must not be null");
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this.refStart = refStart;
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this.loc = loc;
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this.consensusType = consensusType;
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@ -68,10 +77,12 @@ final class ConsensusSpan {
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return loc.getStart() - refStart;
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}
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@Ensures("result >= 0")
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public int getGenomeStart() {
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return loc.getStart();
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}
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@Ensures("result >= 0")
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public int getGenomeStop() {
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return loc.getStop();
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}
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@ -80,13 +91,18 @@ final class ConsensusSpan {
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return consensusType;
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}
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@Ensures("result >= 0")
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public int size() {
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return getGenomeStop() - getGenomeStart() + 1;
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}
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@Ensures("result == !isVariable()")
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public boolean isConserved() { return getConsensusType() == Type.CONSERVED; }
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@Ensures("result == !isConserved()")
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public boolean isVariable() { return getConsensusType() == Type.VARIABLE; }
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@Ensures("result != null")
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public String toString() {
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return String.format("%s %s", consensusType, loc);
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}
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@ -0,0 +1,150 @@
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// our package
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package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
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// the imports for unit testing.
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.gatk.walkers.qc.ValidateBAQWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.baq.BAQ;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.BeforeMethod;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Basic unit test for GenomeLoc
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*/
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public class ConsensusSpanUnitTest extends BaseTest {
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File referenceFile = new File(hg19Reference);
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GenomeLocParser genomeLocParser;
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IndexedFastaSequenceFile fasta;
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GenomeLoc loc;
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@BeforeClass
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public void before() {
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try {
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fasta = new IndexedFastaSequenceFile(referenceFile);
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genomeLocParser = new GenomeLocParser(fasta.getSequenceDictionary());
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loc = genomeLocParser.createGenomeLoc("1", 10, 19);
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}
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catch(FileNotFoundException ex) {
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throw new UserException.CouldNotReadInputFile(referenceFile,ex);
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}
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}
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// private class BAQTest {
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// String readBases, refBases;
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// byte[] quals, expected;
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// String cigar;
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// int refOffset;
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// int pos;
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//
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// public BAQTest(String _refBases, String _readBases, String _quals, String _expected) {
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// this(0, -1, null, _readBases, _refBases, _quals, _expected);
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// }
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//
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// public BAQTest(int refOffset, String _refBases, String _readBases, String _quals, String _expected) {
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// this(refOffset, -1, null, _refBases, _readBases, _quals, _expected);
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// }
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//
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// public BAQTest(long pos, String cigar, String _readBases, String _quals, String _expected) {
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// this(0, pos, cigar, null, _readBases, _quals, _expected);
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// }
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//
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//
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// public BAQTest(int _refOffset, long _pos, String _cigar, String _refBases, String _readBases, String _quals, String _expected) {
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// refOffset = _refOffset;
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// pos = (int)_pos;
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// cigar = _cigar;
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// readBases = _readBases;
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// refBases = _refBases;
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//
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// quals = new byte[_quals.getBytes().length];
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// expected = new byte[_quals.getBytes().length];
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// for ( int i = 0; i < quals.length; i++) {
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// quals[i] = (byte)(_quals.getBytes()[i] - 33);
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// expected[i] = (byte)(_expected.getBytes()[i] - 33);
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// }
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// }
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//
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// public String toString() { return readBases; }
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//
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// public SAMRecord createRead() {
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// SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, pos > 0 ? pos + (refOffset > 0 ? refOffset : 0): 1, readBases.getBytes(), quals);
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// //if ( cigar != null ) read.setAlignmentEnd(readBases.getBytes().length + pos);
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// read.setCigarString( cigar == null ? String.format("%dM", quals.length) : cigar);
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// return read;
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// }
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// }
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@Test(enabled = true)
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public void testType() {
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Assert.assertEquals(ConsensusSpan.Type.CONSERVED, ConsensusSpan.Type.otherType(ConsensusSpan.Type.VARIABLE));
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Assert.assertEquals(ConsensusSpan.Type.VARIABLE, ConsensusSpan.Type.otherType(ConsensusSpan.Type.CONSERVED));
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}
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@Test(enabled = true)
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public void testConsensusSpanOffset0() {
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ConsensusSpan span = new ConsensusSpan(0, loc, ConsensusSpan.Type.CONSERVED);
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Assert.assertEquals(span.getOffsetFromStartOfSites(), 10);
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Assert.assertEquals(span.getGenomeStart(), loc.getStart());
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Assert.assertEquals(span.getGenomeStop(), loc.getStop());
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Assert.assertEquals(span.getConsensusType(), ConsensusSpan.Type.CONSERVED);
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Assert.assertEquals(span.size(), 10);
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}
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@Test(enabled = true)
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public void testConsensusSpanOffset10() {
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ConsensusSpan span = new ConsensusSpan(10, loc, ConsensusSpan.Type.CONSERVED);
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Assert.assertEquals(span.getOffsetFromStartOfSites(), 0);
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Assert.assertEquals(span.getGenomeStart(), loc.getStart());
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Assert.assertEquals(span.getGenomeStop(), loc.getStop());
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Assert.assertEquals(span.getConsensusType(), ConsensusSpan.Type.CONSERVED);
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Assert.assertEquals(span.size(), 10);
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}
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@Test(enabled = true)
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public void testConsensusSpanTypes() {
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ConsensusSpan conserved = new ConsensusSpan(0, loc, ConsensusSpan.Type.CONSERVED);
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Assert.assertEquals(conserved.getConsensusType(), ConsensusSpan.Type.CONSERVED);
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Assert.assertTrue(conserved.isConserved());
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Assert.assertFalse(conserved.isVariable());
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ConsensusSpan variable = new ConsensusSpan(0, loc, ConsensusSpan.Type.VARIABLE);
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Assert.assertEquals(variable.getConsensusType(), ConsensusSpan.Type.VARIABLE);
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Assert.assertFalse(variable.isConserved());
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Assert.assertTrue(variable.isVariable());
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}
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@Test(enabled = true, expectedExceptions = {Error.class, Exception.class})
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public void testBadSpanCreationBadOffset() {
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ConsensusSpan span = new ConsensusSpan(-1, loc, ConsensusSpan.Type.CONSERVED);
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}
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@Test(enabled = true, expectedExceptions = {Error.class, Exception.class})
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public void testBadSpanCreationNullLoc() {
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ConsensusSpan span = new ConsensusSpan(0, null, ConsensusSpan.Type.CONSERVED);
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}
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@Test(enabled = true, expectedExceptions = {Error.class, Exception.class})
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public void testBadSpanCreationNullType() {
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ConsensusSpan span = new ConsensusSpan(0, loc, null);
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}
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}
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