Reorganized the testing code and created ClipReadsTestUtils
Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
*Still needs debugging because code is not working.
Created test classes to be used across several tests.
Some cases are still commented out.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
This commit is contained in:
Roger Zurawicki
Mauricio Carneiro
parent
0e9c2cefa2
commit
4cbd1f0dec
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@ -0,0 +1,18 @@
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package org.broadinstitute.sting.utils.clipreads;
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/**
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* Created by IntelliJ IDEA.
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* User: roger
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* Date: 11/29/11
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* Time: 4:53 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class CigarStringTestPair {
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public String toTest;
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public String expected;
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public CigarStringTestPair(String ToTest, String Expected) {
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this.toTest = ToTest;
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this.expected = Expected;
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}
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}
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@ -0,0 +1,185 @@
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package org.broadinstitute.sting.utils.clipreads;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.TextCigarCodec;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.testng.Assert;
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import java.util.*;
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/**
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* Created by IntelliJ IDEA.
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* User: roger
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* Date: 11/27/11
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* Time: 6:45 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class ClipReadsTestUtils {
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//Should contain all the utils needed for tests to mass produce
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//reads, cigars, and other needed classes
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final static String BASES = "ACTG";
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final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
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public static void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) {
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// Because quals to char start at 33 for visibility
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baseQuals = subtractToArray(baseQuals, 33);
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Assert.assertEquals(read.getReadBases(), readBases);
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Assert.assertEquals(read.getBaseQualities(), baseQuals);
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Assert.assertEquals(read.getCigarString(), cigar);
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}
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public static void testCigar(GATKSAMRecord read, String cigar) {
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Assert.assertEquals(read.getCigarString(), cigar);
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}
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public static void testBaseQual(GATKSAMRecord read, byte[] readBases, byte[] baseQuals) {
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// Because quals to chars start at 33 for visibility
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baseQuals = subtractToArray(baseQuals, 33);
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if (readBases.length > 0 && baseQuals.length > 0) {
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Assert.assertEquals(read.getReadBases(), readBases);
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Assert.assertEquals(read.getBaseQualities(), baseQuals);
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} else
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Assert.assertTrue(read.isEmpty());
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}
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private static byte[] subtractToArray(byte[] array, int n) {
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if (array == null)
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return null;
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byte[] output = new byte[array.length];
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for (int i = 0; i < array.length; i++)
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output[i] = (byte) (array[i] - n);
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return output;
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}
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// What the test read looks like
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// Ref: 10 11 12 13 14 15 16 17
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// Read: 0 1 2 3 - - - -
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// --------------------------------
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// Bases: A C T G - - - -
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// Quals: ! + 5 ? - - - -
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public static GATKSAMRecord makeRead() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
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GATKSAMRecord output = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, BASES.length());
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output.setReadBases(new String(BASES).getBytes());
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output.setBaseQualityString(new String(QUALS));
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return output;
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}
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public static GATKSAMRecord makeReadFromCigar(Cigar cigar) {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
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GATKSAMRecord output = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, cigar.getReadLength());
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output.setReadBases(cycleString(BASES, cigar.getReadLength()).getBytes());
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output.setBaseQualityString(cycleString(QUALS, cigar.getReadLength()));
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output.setCigar(cigar);
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return output;
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}
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private static String cycleString(String string, int length) {
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String output = "";
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int cycles = (length / string.length()) + 1;
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for (int i = 1; i < cycles; i++)
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output += string;
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for (int j = 0; output.length() < length; j++)
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output += string.charAt(j % string.length());
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return output;
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}
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public static Set<Cigar> generateCigars() {
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// This function generates every permutation of cigar strings we need.
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LinkedHashSet<Cigar> output = new LinkedHashSet<Cigar>();
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List<Cigar> clippingOptionsStart = new LinkedList<Cigar>();
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clippingOptionsStart.add(new Cigar());
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clippingOptionsStart.add(TextCigarCodec.getSingleton().decode("1H1S"));
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clippingOptionsStart.add(TextCigarCodec.getSingleton().decode("1S"));
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clippingOptionsStart.add(TextCigarCodec.getSingleton().decode("1H"));
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LinkedList<Cigar> clippingOptionsEnd = new LinkedList<Cigar>();
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clippingOptionsEnd.add(new Cigar());
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clippingOptionsEnd.add(TextCigarCodec.getSingleton().decode("1S1H"));
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clippingOptionsEnd.add(TextCigarCodec.getSingleton().decode("1S"));
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clippingOptionsEnd.add(TextCigarCodec.getSingleton().decode("1H"));
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LinkedList<Cigar> indelOptions1 = new LinkedList<Cigar>();
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indelOptions1.add(new Cigar());
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//indelOptions1.add( TextCigarCodec.getSingleton().decode("1I1D"));
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//indelOptions1.add( TextCigarCodec.getSingleton().decode("1D1I") );
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indelOptions1.add(TextCigarCodec.getSingleton().decode("1I"));
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indelOptions1.add(TextCigarCodec.getSingleton().decode("1D"));
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LinkedList<Cigar> indelOptions2 = new LinkedList<Cigar>();
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indelOptions2.add(new Cigar());
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indelOptions2.add(TextCigarCodec.getSingleton().decode("1I"));
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indelOptions2.add(null);
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// Start With M as base CigarElements, M,
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LinkedList<Cigar> base = new LinkedList<Cigar>();
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base.add(TextCigarCodec.getSingleton().decode("1M"));
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base.add(TextCigarCodec.getSingleton().decode("5M"));
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base.add(TextCigarCodec.getSingleton().decode("25M"));
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// Should indel be added as a base?
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// Nested loops W00t!
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for (Cigar Base : base) {
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for (Cigar indelStart : indelOptions1) {
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for (Cigar indelEnd : indelOptions2) {
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for (Cigar clipStart : clippingOptionsStart) {
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for (Cigar clipEnd : clippingOptionsEnd) {
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// Create a list of Cigar Elements and construct Cigar
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List<CigarElement> CigarBuilder = new ArrayList<CigarElement>();
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// add starting clipping (H/S)
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CigarBuilder.addAll(clipStart.getCigarElements());
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// add first base (M)
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CigarBuilder.addAll(Base.getCigarElements());
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// add first indel
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CigarBuilder.addAll(indelStart.getCigarElements());
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// add second base (M)
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CigarBuilder.addAll(Base.getCigarElements());
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// add another indel or nothing (M)
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if (indelEnd != null)
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CigarBuilder.addAll(indelEnd.getCigarElements());
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// add final clipping (S/H)
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CigarBuilder.addAll(clipEnd.getCigarElements());
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output.add(new Cigar(removeConsecutiveElements(CigarBuilder)));
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}
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}
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}
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}
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}
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return output;
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}
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private static List<CigarElement> removeConsecutiveElements(List<CigarElement> cigarBuilder) {
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LinkedList<CigarElement> output = new LinkedList<CigarElement>();
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for (CigarElement E : cigarBuilder) {
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if (output.isEmpty() || output.getLast().getOperator() != E.getOperator())
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output.add(E);
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}
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return output;
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}
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}
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@ -0,0 +1,69 @@
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package org.broadinstitute.sting.utils.clipreads;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.testng.annotations.BeforeTest;
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import org.testng.annotations.Test;
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import java.util.LinkedList;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: roger
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* Date: 11/27/11
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* Time: 5:17 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class ClippingOpUnitTest extends BaseTest {
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ClippingOp clippingOp;
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GATKSAMRecord read;
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@BeforeTest
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public void init() {
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read = ClipReadsTestUtils.makeRead();
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}
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@Test
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private void testHardClip() {
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List<TestParameter> testList = new LinkedList<TestParameter>();
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testList.add(new TestParameter(0, 0, 1, 4, "1H3M"));//clip 1 base at start
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testList.add(new TestParameter(3, 3, 0, 3, "3M1H"));//clip 1 base at end
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testList.add(new TestParameter(0, 1, 2, 4, "2H2M"));//clip 2 bases at start
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testList.add(new TestParameter(2, 3, 0, 2, "2M2H"));//clip 2 bases at end
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testList.add(new TestParameter(0, 2, 3, 4, "3H1M"));//clip 3 bases at start
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testList.add(new TestParameter(1, 3, 0, 1, "1M3H"));//clip 3 bases at end
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for (TestParameter p : testList) {
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init();
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clippingOp = new ClippingOp(p.inputStart, p.inputStop);
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logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.substringStart + "," + p.substringStop + "," + p.cigar);
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ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.HARDCLIP_BASES, read),
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ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
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ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
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p.cigar);
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}
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}
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@Test
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private void testSoftClip() {
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List<TestParameter> testList = new LinkedList<TestParameter>();
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testList.add(new TestParameter(0, 0, -1, -1, "1S3M"));//clip 1 base at start
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testList.add(new TestParameter(3, 3, -1, -1, "3M1S"));//clip 1 base at end
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testList.add(new TestParameter(0, 1, -1, -1, "2S2M"));//clip 2 bases at start
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testList.add(new TestParameter(2, 3, -1, -1, "2M2S"));//clip 2 bases at end
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testList.add(new TestParameter(0, 2, -1, -1, "3S1M"));//clip 3 bases at start
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testList.add(new TestParameter(1, 3, -1, -1, "1M3S"));//clip 3 bases at end
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for (TestParameter p : testList) {
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init();
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clippingOp = new ClippingOp(p.inputStart, p.inputStop);
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logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.cigar);
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ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.SOFTCLIP_BASES, read),
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ClipReadsTestUtils.BASES.getBytes(), ClipReadsTestUtils.QUALS.getBytes(), p.cigar);
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}
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}
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}
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@ -25,16 +25,19 @@
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package org.broadinstitute.sting.utils.clipreads;
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import net.sf.samtools.*;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import net.sf.samtools.TextCigarCodec;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.testng.Assert;
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import org.testng.annotations.BeforeMethod;
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import org.testng.annotations.Test;
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import java.util.*;
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import java.util.LinkedList;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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@ -47,212 +50,205 @@ public class ReadClipperUnitTest extends BaseTest {
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// TODO: exception testing, make cases that should fail will fail
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//int debug = 0;
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// TODO: add indels to all test cases
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GATKSAMRecord read, expected;
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ReadClipper readClipper;
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final static String BASES = "ACTG";
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final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
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private void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) {
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// Because quals to char start at 33 for visibility
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baseQuals = subtractToArray(baseQuals, 33);
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Assert.assertEquals(read.getReadBases(), readBases);
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Assert.assertEquals(read.getBaseQualities(), baseQuals);
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Assert.assertEquals(read.getCigarString(), cigar);
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}
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private void testBaseQual(GATKSAMRecord read, byte[] readBases, byte[] baseQuals) {
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// Because quals to chars start at 33 for visibility
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baseQuals = subtractToArray(baseQuals, 33);
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if ( readBases.length > 0 && baseQuals.length > 0 ) {
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Assert.assertEquals(read.getReadBases(), readBases);
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Assert.assertEquals(read.getBaseQualities(), baseQuals);
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}
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else
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Assert.assertTrue(read.isEmpty());
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}
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public class testParameter {
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int inputStart;
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int inputStop;
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int substringStart;
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int substringStop;
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String cigar;
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public testParameter(int InputStart, int InputStop, int SubstringStart, int SubstringStop, String Cigar) {
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inputStart = InputStart;
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inputStop = InputStop;
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substringStart = SubstringStart;
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substringStop = SubstringStop;
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cigar = Cigar;
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}
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}
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private byte[] subtractToArray (byte[] array, int n ) {
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if ( array == null)
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return null;
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byte[] output = new byte[array.length];
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for ( int i = 0; i < array.length; i++)
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output[i] = (byte) ( array[i] - n );
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return output;
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}
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// What the test read looks like
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// Ref: 1 2 3 4 5 6 7 8
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// Read: 0 1 2 3 - - - -
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// -----------------------------
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// Bases: A C T G - - - -
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// Quals: ! + 5 ? - - - -
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@BeforeMethod
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public void init() {
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SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
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read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
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read.setReadBases(new String(BASES).getBytes());
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read.setBaseQualityString(new String(QUALS));
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readClipper = new ReadClipper(read);
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//logger.warn(read.getCigarString());
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readClipper = new ReadClipper(ClipReadsTestUtils.makeRead());
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}
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@Test ( enabled = true )
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@Test(enabled = true)
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public void testHardClipBothEndsByReferenceCoordinates() {
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logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
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//int debug = 1;
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//Clip whole read
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Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(1,1), new GATKSAMRecord(read.getHeader()));
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Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(10, 10), new GATKSAMRecord(readClipper.read.getHeader()));
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//clip 1 base
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expected = readClipper.hardClipBothEndsByReferenceCoordinates(1,4);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3));
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Assert.assertEquals(expected.getCigarString(), "1H2M1H");
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ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipBothEndsByReferenceCoordinates(10, 13),
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ClipReadsTestUtils.BASES.substring(1, 3).getBytes(), ClipReadsTestUtils.QUALS.substring(1, 3).getBytes(),
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"1H2M1H");
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List<CigarStringTestPair> cigarStringTestPairs = new LinkedList<CigarStringTestPair>();
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cigarStringTestPairs.add(new CigarStringTestPair("5M1D1M2I4M5I6M1D3M2I100M", "1H4M1D1M2I4M5I6M1D3M2I99M1H"));
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//cigarStringTestPairs.add( new CigarStringTestPair("5M1I1M2I1M","1H4M1I1M2I1H"));
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cigarStringTestPairs.add(new CigarStringTestPair("1S1M1I1M1I1M1I1M1I1M1I1M1S", "1H1M1I1M1I1M1I1M1I1M1I1M1H"));
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cigarStringTestPairs.add(new CigarStringTestPair("1S1M1D1M1D1M1D1M1D1M1D1M1S", "1H1M1D1M1D1M1D1M1D1M1D1M1H"));
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for (CigarStringTestPair pair : cigarStringTestPairs) {
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readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar(TextCigarCodec.getSingleton().decode(pair.toTest)));
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ClipReadsTestUtils.testCigar(readClipper.hardClipBothEndsByReferenceCoordinates(
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ReadUtils.getRefCoordSoftUnclippedStart(readClipper.read),
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ReadUtils.getRefCoordSoftUnclippedEnd(readClipper.read)),
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pair.expected);
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}
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/*
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for ( Cigar cigar: ClipReadsTestUtils.generateCigars() ) {
|
||||
// The read has to be long enough to clip one base from each side
|
||||
// This also filters a lot of cigars
|
||||
if ( cigar.getReadLength() > 26 ) {
|
||||
readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar( cigar ));
|
||||
System.out.println( "Testing Cigar: "+cigar.toString() ) ;
|
||||
//cigar length reference plus soft clip
|
||||
|
||||
ClipReadsTestUtils.testBaseQual(
|
||||
readClipper.hardClipBothEndsByReferenceCoordinates(
|
||||
ReadUtils.getRefCoordSoftUnclippedStart(readClipper.read),
|
||||
ReadUtils.getRefCoordSoftUnclippedEnd(readClipper.read) ),
|
||||
readClipper.read.getReadString().substring(1, (cigar.getReadLength() - 1)).getBytes(),
|
||||
readClipper.read.getBaseQualityString().substring(1, (cigar.getReadLength() - 1)).getBytes());
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipByReadCoordinates() {
|
||||
|
||||
logger.warn("Executing testHardClipByReadCoordinates");
|
||||
|
||||
//Clip whole read
|
||||
Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader()));
|
||||
Assert.assertEquals(readClipper.hardClipByReadCoordinates(0, 3), new GATKSAMRecord(readClipper.read.getHeader()));
|
||||
|
||||
List<testParameter> testList = new LinkedList<testParameter>();
|
||||
testList.add(new testParameter(0,0,1,4,"1H3M"));//clip 1 base at start
|
||||
testList.add(new testParameter(3,3,0,3,"3M1H"));//clip 1 base at end
|
||||
testList.add(new testParameter(0,1,2,4,"2H2M"));//clip 2 bases at start
|
||||
testList.add(new testParameter(2,3,0,2,"2M2H"));//clip 2 bases at end
|
||||
List<TestParameter> testList = new LinkedList<TestParameter>();
|
||||
testList.add(new TestParameter(0, 0, 1, 4, "1H3M"));//clip 1 base at start
|
||||
testList.add(new TestParameter(3, 3, 0, 3, "3M1H"));//clip 1 base at end
|
||||
testList.add(new TestParameter(0, 1, 2, 4, "2H2M"));//clip 2 bases at start
|
||||
testList.add(new TestParameter(2, 3, 0, 2, "2M2H"));//clip 2 bases at end
|
||||
|
||||
for ( testParameter p : testList ) {
|
||||
for (TestParameter p : testList) {
|
||||
init();
|
||||
//logger.warn("Testing Parameters: " + p.inputStart+","+p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
|
||||
testBaseQualCigar(readClipper.hardClipByReadCoordinates(p.inputStart, p.inputStop),
|
||||
BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReadCoordinates(p.inputStart, p.inputStop),
|
||||
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
p.cigar);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipByReferenceCoordinates() {
|
||||
logger.warn("Executing testHardClipByReferenceCoordinates");
|
||||
//logger.warn(debug);
|
||||
//Clip whole read
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new GATKSAMRecord(read.getHeader()));
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(10, 13), new GATKSAMRecord(readClipper.read.getHeader()));
|
||||
|
||||
List<testParameter> testList = new LinkedList<testParameter>();
|
||||
testList.add(new testParameter(-1,1,1,4,"1H3M"));//clip 1 base at start
|
||||
testList.add(new testParameter(4,-1,0,3,"3M1H"));//clip 1 base at end
|
||||
testList.add(new testParameter(-1,2,2,4,"2H2M"));//clip 2 bases at start
|
||||
testList.add(new testParameter(3,-1,0,2,"2M2H"));//clip 2 bases at end
|
||||
List<TestParameter> testList = new LinkedList<TestParameter>();
|
||||
testList.add(new TestParameter(-1, 10, 1, 4, "1H3M"));//clip 1 base at start
|
||||
testList.add(new TestParameter(13, -1, 0, 3, "3M1H"));//clip 1 base at end
|
||||
testList.add(new TestParameter(-1, 11, 2, 4, "2H2M"));//clip 2 bases at start
|
||||
testList.add(new TestParameter(12, -1, 0, 2, "2M2H"));//clip 2 bases at end
|
||||
|
||||
for ( testParameter p : testList ) {
|
||||
for (TestParameter p : testList) {
|
||||
init();
|
||||
//logger.warn("Testing Parameters: " + p.inputStart+","+p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
|
||||
testBaseQualCigar(readClipper.hardClipByReferenceCoordinates(p.inputStart, p.inputStop),
|
||||
BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinates(p.inputStart, p.inputStop),
|
||||
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
p.cigar);
|
||||
}
|
||||
|
||||
List<CigarStringTestPair> cigarStringTestPairs = new LinkedList<CigarStringTestPair>();
|
||||
cigarStringTestPairs.add(new CigarStringTestPair("5M1D1M2I4M5I6M1D3M2I100M", "1H4M1D1M2I4M5I6M1D3M2I100M"));
|
||||
//cigarStringTestPairs.add( new CigarStringTestPair("5M1I1M2I1M","1H4M1I1M2I1M"));
|
||||
cigarStringTestPairs.add(new CigarStringTestPair("1S1M1I1M1I1M1I1M1I1M1I1M1S", "1H1M1I1M1I1M1I1M1I1M1I1M1S"));
|
||||
cigarStringTestPairs.add(new CigarStringTestPair("1S1M1D1M1D1M1D1M1D1M1D1M1S", "1H1M1D1M1D1M1D1M1D1M1D1M1S"));
|
||||
|
||||
//Clips only first base
|
||||
for (CigarStringTestPair pair : cigarStringTestPairs) {
|
||||
readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar(TextCigarCodec.getSingleton().decode(pair.toTest)));
|
||||
ClipReadsTestUtils.testCigar(readClipper.hardClipByReadCoordinates(0, 0), pair.expected);
|
||||
}
|
||||
/*
|
||||
for ( Cigar cigar: ClipReadsTestUtils.generateCigars() ) {
|
||||
// The read has to be long enough to clip one base
|
||||
// This also filters a lot of cigars
|
||||
if ( cigar.getReadLength() > 26 ) {
|
||||
readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar( cigar ));
|
||||
System.out.println( "Testing Cigar: "+cigar.toString() ) ;
|
||||
//cigar length reference plus soft clip
|
||||
|
||||
// Clip first read
|
||||
ClipReadsTestUtils.testBaseQual(
|
||||
readClipper.hardClipByReadCoordinates(0,0),
|
||||
readClipper.read.getReadString().substring(1, cigar.getReadLength()).getBytes(),
|
||||
readClipper.read.getBaseQualityString().substring(1, cigar.getReadLength()).getBytes());
|
||||
}
|
||||
}
|
||||
*/
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipByReferenceCoordinatesLeftTail() {
|
||||
init();
|
||||
logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail");
|
||||
|
||||
//Clip whole read
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader()));
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(13), new GATKSAMRecord(readClipper.read.getHeader()));
|
||||
|
||||
List<testParameter> testList = new LinkedList<testParameter>();
|
||||
testList.add(new testParameter(1, -1, 1, 4, "1H3M"));//clip 1 base at start
|
||||
testList.add(new testParameter(2, -1, 2, 4, "2H2M"));//clip 2 bases at start
|
||||
List<TestParameter> testList = new LinkedList<TestParameter>();
|
||||
testList.add(new TestParameter(10, -1, 1, 4, "1H3M"));//clip 1 base at start
|
||||
testList.add(new TestParameter(11, -1, 2, 4, "2H2M"));//clip 2 bases at start
|
||||
|
||||
for ( testParameter p : testList ) {
|
||||
for (TestParameter p : testList) {
|
||||
init();
|
||||
//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
|
||||
testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesLeftTail(p.inputStart),
|
||||
BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesLeftTail(p.inputStart),
|
||||
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
p.cigar);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipByReferenceCoordinatesRightTail() {
|
||||
init();
|
||||
logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
|
||||
|
||||
//Clip whole read
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader()));
|
||||
Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(10), new GATKSAMRecord(readClipper.read.getHeader()));
|
||||
|
||||
List<testParameter> testList = new LinkedList<testParameter>();
|
||||
testList.add(new testParameter(-1, 4, 0, 3, "3M1H"));//clip 1 base at end
|
||||
testList.add(new testParameter(-1, 3, 0, 2, "2M2H"));//clip 2 bases at end
|
||||
List<TestParameter> testList = new LinkedList<TestParameter>();
|
||||
testList.add(new TestParameter(-1, 13, 0, 3, "3M1H"));//clip 1 base at end
|
||||
testList.add(new TestParameter(-1, 12, 0, 2, "2M2H"));//clip 2 bases at end
|
||||
|
||||
for ( testParameter p : testList ) {
|
||||
for (TestParameter p : testList) {
|
||||
init();
|
||||
//logger.warn("Testing Parameters: " + p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
|
||||
testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesRightTail(p.inputStop),
|
||||
BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesRightTail(p.inputStop),
|
||||
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
p.cigar);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipLowQualEnds() {
|
||||
// Needs a thorough redesign
|
||||
logger.warn("Executing testHardClipByReferenceCoordinates");
|
||||
|
||||
//Clip whole read
|
||||
Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new GATKSAMRecord(read.getHeader()));
|
||||
Assert.assertEquals(readClipper.hardClipLowQualEnds((byte) 64), new GATKSAMRecord(readClipper.read.getHeader()));
|
||||
|
||||
List<testParameter> testList = new LinkedList<testParameter>();
|
||||
testList.add(new testParameter(1,-1,1,4,"1H3M"));//clip 1 base at start
|
||||
testList.add(new testParameter(11,-1,2,4,"2H2M"));//clip 2 bases at start
|
||||
List<TestParameter> testList = new LinkedList<TestParameter>();
|
||||
testList.add(new TestParameter(1, -1, 1, 4, "1H3M"));//clip 1 base at start
|
||||
testList.add(new TestParameter(11, -1, 2, 4, "2H2M"));//clip 2 bases at start
|
||||
|
||||
for ( testParameter p : testList ) {
|
||||
for (TestParameter p : testList) {
|
||||
init();
|
||||
//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
|
||||
testBaseQualCigar(readClipper.hardClipLowQualEnds((byte) p.inputStart),
|
||||
BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipLowQualEnds((byte) p.inputStart),
|
||||
ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
|
||||
p.cigar);
|
||||
}
|
||||
/* todo find a better way to test lowqual tail clipping on both sides
|
||||
/* todo find a better way to test lowqual tail clipping on both sides
|
||||
// Reverse Quals sequence
|
||||
readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
|
||||
|
||||
|
|
@ -272,127 +268,13 @@ public class ReadClipperUnitTest extends BaseTest {
|
|||
*/
|
||||
}
|
||||
|
||||
// public class ReadMaker {
|
||||
//Should have functions that can
|
||||
// make basic read
|
||||
// make reads by cigar,
|
||||
// and by quals,
|
||||
// package in a readclipper
|
||||
// This has been already done in the current class
|
||||
// GATKSAMRecord read;
|
||||
// ReadClipper readClipper;
|
||||
|
||||
public String cycleString ( String string, int length ) {
|
||||
String output = "";
|
||||
int cycles = ( length / string.length() ) + 1;
|
||||
|
||||
for ( int i = 1; i < cycles; i++ )
|
||||
output += string;
|
||||
|
||||
for ( int j = 0; output.length() < length; j++ )
|
||||
output += string.charAt( j % string.length() );
|
||||
|
||||
return output;
|
||||
|
||||
}
|
||||
|
||||
private void makeFromCigar( Cigar cigar ) {
|
||||
readClipper = null;
|
||||
read = null;
|
||||
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
|
||||
read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, cigar.getReadLength());
|
||||
read.setReadBases(cycleString(BASES, cigar.getReadLength()).getBytes());
|
||||
read.setBaseQualityString( cycleString(QUALS, cigar.getReadLength() ));
|
||||
read.setCigar(cigar);
|
||||
readClipper = new ReadClipper(read);
|
||||
}
|
||||
|
||||
// }
|
||||
|
||||
private Set<Cigar> generateCigars() {
|
||||
|
||||
// This function generates every permutation of cigar strings we need.
|
||||
|
||||
LinkedHashSet<Cigar> output = new LinkedHashSet<Cigar>();
|
||||
|
||||
List<Cigar> clippingOptionsStart = new LinkedList<Cigar>();
|
||||
clippingOptionsStart.add( new Cigar() );
|
||||
clippingOptionsStart.add( TextCigarCodec.getSingleton().decode("1H1S") );
|
||||
clippingOptionsStart.add( TextCigarCodec.getSingleton().decode("1S") );
|
||||
clippingOptionsStart.add( TextCigarCodec.getSingleton().decode("1H") );
|
||||
|
||||
LinkedList<Cigar> clippingOptionsEnd = new LinkedList<Cigar>();
|
||||
clippingOptionsEnd.add( new Cigar() );
|
||||
clippingOptionsEnd.add( TextCigarCodec.getSingleton().decode("1S1H") );
|
||||
clippingOptionsEnd.add( TextCigarCodec.getSingleton().decode("1S"));
|
||||
clippingOptionsEnd.add( TextCigarCodec.getSingleton().decode("1H"));
|
||||
|
||||
|
||||
LinkedList<Cigar> indelOptions = new LinkedList<Cigar>();
|
||||
indelOptions.add( new Cigar() );
|
||||
//indelOptions.add( TextCigarCodec.getSingleton().decode("1I1D"));
|
||||
//indelOptions.add( TextCigarCodec.getSingleton().decode("1D1I") );
|
||||
indelOptions.add( TextCigarCodec.getSingleton().decode("1I") );
|
||||
indelOptions.add( TextCigarCodec.getSingleton().decode("1D") );
|
||||
|
||||
// Start With M as base CigarElements, M,
|
||||
|
||||
LinkedList<Cigar> base = new LinkedList<Cigar>();
|
||||
base.add( TextCigarCodec.getSingleton().decode("1M"));
|
||||
base.add( TextCigarCodec.getSingleton().decode("5M"));
|
||||
base.add( TextCigarCodec.getSingleton().decode("25M"));
|
||||
// Should indel be added as a base?
|
||||
|
||||
// Nested loops W00t!
|
||||
for ( Cigar Base : base) {
|
||||
for ( Cigar indelStart: indelOptions) {
|
||||
for ( Cigar indelEnd: indelOptions) {
|
||||
for ( Cigar clipStart: clippingOptionsStart) {
|
||||
for ( Cigar clipEnd: clippingOptionsEnd) {
|
||||
// Create a list of Cigar Elements and construct Cigar
|
||||
List<CigarElement> CigarBuilder = new ArrayList<CigarElement>();
|
||||
CigarBuilder.addAll(Base.getCigarElements());
|
||||
CigarBuilder.addAll(indelStart.getCigarElements());
|
||||
CigarBuilder.addAll(Base.getCigarElements());
|
||||
CigarBuilder.addAll(indelEnd.getCigarElements());
|
||||
CigarBuilder.addAll(clipEnd.getCigarElements());
|
||||
//CigarBuilder.addAll(0, indelStart.getCigarElements());
|
||||
CigarBuilder.addAll(0, clipStart.getCigarElements());
|
||||
//System.out.println( new Cigar( removeConsecutiveElements(CigarBuilder) ).toString() );
|
||||
output.add( new Cigar( removeConsecutiveElements(CigarBuilder) ) );
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return output;
|
||||
}
|
||||
|
||||
private List<CigarElement> removeConsecutiveElements(List<CigarElement> cigarBuilder) {
|
||||
LinkedList<CigarElement> output = new LinkedList<CigarElement>();
|
||||
for ( CigarElement E: cigarBuilder ) {
|
||||
if ( output.isEmpty() || output.getLast().getOperator() != E.getOperator())
|
||||
output.add(E);
|
||||
}
|
||||
return output;
|
||||
}
|
||||
|
||||
@Test ( enabled = true )
|
||||
@Test(enabled = true)
|
||||
public void testHardClipSoftClippedBases() {
|
||||
|
||||
// Generate a list of cigars to test
|
||||
for ( Cigar cigar: generateCigars() ) {
|
||||
for (Cigar cigar : ClipReadsTestUtils.generateCigars()) {
|
||||
//logger.warn("Testing Cigar: "+cigar.toString());
|
||||
makeFromCigar( cigar );
|
||||
|
||||
|
||||
try {
|
||||
readClipper.hardClipLeadingInsertions();
|
||||
}
|
||||
catch ( ReviewedStingException e ) {}
|
||||
|
||||
readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar(cigar));
|
||||
|
||||
int clipStart = 0;
|
||||
int clipEnd = 0;
|
||||
|
|
@ -401,41 +283,38 @@ public class ReadClipperUnitTest extends BaseTest {
|
|||
List<CigarElement> cigarElements = cigar.getCigarElements();
|
||||
int CigarListLength = cigarElements.size();
|
||||
|
||||
|
||||
// It will know what needs to be clipped based on the start and end of the string, hardclips and softclips
|
||||
// are added to the amount to clip
|
||||
if ( cigarElements.get(0).getOperator() == CigarOperator.HARD_CLIP ) {
|
||||
if (cigarElements.get(0).getOperator() == CigarOperator.HARD_CLIP) {
|
||||
//clipStart += cigarElements.get(0).getLength();
|
||||
if ( cigarElements.get(1).getOperator() == CigarOperator.SOFT_CLIP ) {
|
||||
if (cigarElements.get(1).getOperator() == CigarOperator.SOFT_CLIP) {
|
||||
clipStart += cigarElements.get(1).getLength();
|
||||
// Check for leading indel
|
||||
if ( cigarElements.get(2).getOperator() == CigarOperator.INSERTION ) {
|
||||
if (cigarElements.get(2).getOperator() == CigarOperator.INSERTION) {
|
||||
expectEmptyRead = true;
|
||||
}
|
||||
}
|
||||
// Check for leading indel
|
||||
else if ( cigarElements.get(1).getOperator() == CigarOperator.INSERTION ) {
|
||||
else if (cigarElements.get(1).getOperator() == CigarOperator.INSERTION) {
|
||||
expectEmptyRead = true;
|
||||
}
|
||||
}
|
||||
else if ( cigarElements.get(0).getOperator() == CigarOperator.SOFT_CLIP ) {
|
||||
} else if (cigarElements.get(0).getOperator() == CigarOperator.SOFT_CLIP) {
|
||||
clipStart += cigarElements.get(0).getLength();
|
||||
// Check for leading indel
|
||||
if ( cigarElements.get(1).getOperator() == CigarOperator.INSERTION ) {
|
||||
if (cigarElements.get(1).getOperator() == CigarOperator.INSERTION) {
|
||||
expectEmptyRead = true;
|
||||
}
|
||||
}
|
||||
//Check for leading indel
|
||||
else if ( cigarElements.get(0).getOperator() == CigarOperator.INSERTION ) {
|
||||
expectEmptyRead = true;
|
||||
}
|
||||
|
||||
if ( cigarElements.get(CigarListLength - 1).getOperator() == CigarOperator.HARD_CLIP ) {
|
||||
//clipEnd += cigarElements.get(CigarListLength - 1).getLength();
|
||||
if ( cigarElements.get(CigarListLength - 2).getOperator() == CigarOperator.SOFT_CLIP )
|
||||
clipEnd += cigarElements.get(CigarListLength - 2).getLength();
|
||||
else if (cigarElements.get(0).getOperator() == CigarOperator.INSERTION) {
|
||||
expectEmptyRead = true;
|
||||
}
|
||||
else if ( cigarElements.get(CigarListLength - 1).getOperator() == CigarOperator.SOFT_CLIP )
|
||||
|
||||
if (cigarElements.get(CigarListLength - 1).getOperator() == CigarOperator.HARD_CLIP) {
|
||||
//clipEnd += cigarElements.get(CigarListLength - 1).getLength();
|
||||
if (cigarElements.get(CigarListLength - 2).getOperator() == CigarOperator.SOFT_CLIP)
|
||||
clipEnd += cigarElements.get(CigarListLength - 2).getLength();
|
||||
} else if (cigarElements.get(CigarListLength - 1).getOperator() == CigarOperator.SOFT_CLIP)
|
||||
clipEnd += cigarElements.get(CigarListLength - 1).getLength();
|
||||
|
||||
String readBases = readClipper.read.getReadString();
|
||||
|
|
@ -448,15 +327,15 @@ public class ReadClipperUnitTest extends BaseTest {
|
|||
baseQuals = "";
|
||||
|
||||
logger.warn(String.format("Testing cigar %s, expecting Base: %s and Qual: %s",
|
||||
cigar.toString(), readBases.substring( clipStart, readBases.length() - clipEnd ),
|
||||
baseQuals.substring( clipStart, baseQuals.length() - clipEnd ) ) );
|
||||
cigar.toString(), readBases.substring(clipStart, readBases.length() - clipEnd),
|
||||
baseQuals.substring(clipStart, baseQuals.length() - clipEnd)));
|
||||
//if (expectEmptyRead)
|
||||
// testBaseQual( readClipper.hardClipSoftClippedBases(), new byte[0], new byte[0] );
|
||||
//else
|
||||
testBaseQual(readClipper.hardClipSoftClippedBases(),
|
||||
readBases.substring( clipStart, readBases.length() - clipEnd ).getBytes(),
|
||||
baseQuals.substring( clipStart, baseQuals.length() - clipEnd ).getBytes());
|
||||
logger.warn("Cigar: "+cigar.toString()+" PASSED!");
|
||||
ClipReadsTestUtils.testBaseQual(readClipper.hardClipSoftClippedBases(),
|
||||
readBases.substring(clipStart, readBases.length() - clipEnd).getBytes(),
|
||||
baseQuals.substring(clipStart, baseQuals.length() - clipEnd).getBytes());
|
||||
logger.warn("Cigar: " + cigar.toString() + " PASSED!");
|
||||
}
|
||||
// We will use testParameter in the following way
|
||||
// Right tail, left tail,
|
||||
|
|
|
|||
|
|
@ -0,0 +1,24 @@
|
|||
package org.broadinstitute.sting.utils.clipreads;
|
||||
|
||||
/**
|
||||
* Created by IntelliJ IDEA.
|
||||
* User: roger
|
||||
* Date: 11/28/11
|
||||
* Time: 4:07 PM
|
||||
* To change this template use File | Settings | File Templates.
|
||||
*/
|
||||
public class TestParameter {
|
||||
int inputStart;
|
||||
int inputStop;
|
||||
int substringStart;
|
||||
int substringStop;
|
||||
String cigar;
|
||||
|
||||
public TestParameter(int InputStart, int InputStop, int SubstringStart, int SubstringStop, String Cigar) {
|
||||
inputStart = InputStart;
|
||||
inputStop = InputStop;
|
||||
substringStart = SubstringStart;
|
||||
substringStop = SubstringStop;
|
||||
cigar = Cigar;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue