Added more basic UnitTests for ReadClipper
hardClipByReadCoordinatesWorks hardClipLowQualTailsWorks
This commit is contained in:
Roger Zurawicki
parent
8e91e19229
commit
284430d61d
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@ -30,8 +30,7 @@ import org.broadinstitute.sting.BaseTest;
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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 org.testng.annotations.BeforeTest;
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import org.testng.annotations.Test;
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import org.testng.annotations.*;
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import java.util.LinkedList;
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import java.util.List;
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@ -47,7 +46,6 @@ public class ReadClipperUnitTest extends BaseTest {
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// TODO: Add error messages on failed tests
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//int debug = 0;
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GATKSAMRecord read, expected;
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@ -55,73 +53,6 @@ public class ReadClipperUnitTest extends BaseTest {
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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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// 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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@BeforeTest
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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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}
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@Test ( enabled = true )
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public void testHardClipBothEndsByReferenceCoordinates() {
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init();
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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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//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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}
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@Test ( enabled = false ) // TODO This fails at hardClipCigar and returns a NullPointerException
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public void testHardClipByReadCoordinates() {
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init();
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logger.warn("Executing testHardClipByReadCoordinates");
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//Clip whole read
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Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader()));
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//clip 1 base at start
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System.out.println(readClipper.read.getCigarString());
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expected = readClipper.hardClipByReadCoordinates(0,0);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4));
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Assert.assertEquals(expected.getCigarString(), "1H3M");
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//clip 1 base at end
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expected = readClipper.hardClipByReadCoordinates(3,3);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3));
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Assert.assertEquals(expected.getCigarString(), "3M1H");
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//clip 2 bases at start
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expected = readClipper.hardClipByReadCoordinates(0,1);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4));
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Assert.assertEquals(expected.getCigarString(), "2H2M");
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//clip 2 bases at end
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expected = readClipper.hardClipByReadCoordinates(2,3);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2));
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Assert.assertEquals(expected.getCigarString(), "2M2H");
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}
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public void testIfEqual( GATKSAMRecord read, byte[] readBases, String baseQuals, String cigar) {
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Assert.assertEquals(read.getReadBases(), readBases);
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@ -145,6 +76,65 @@ public class ReadClipperUnitTest extends BaseTest {
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}
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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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}
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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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//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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}
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@Test ( enabled = true )
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public void testHardClipByReadCoordinates() {
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logger.warn("Executing testHardClipByReadCoordinates");
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//Clip whole read
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Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader()));
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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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for ( testParameter p : testList ) {
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init();
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//logger.warn("Testing Parameters: " + p.inputStart+","+p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar);
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testIfEqual( readClipper.hardClipByReadCoordinates(p.inputStart, p.inputStop),
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BASES.substring(p.substringStart,p.substringStop).getBytes(),
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QUALS.substring(p.substringStart,p.substringStop),
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p.cigar );
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}
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}
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@Test ( enabled = true )
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public void testHardClipByReferenceCoordinates() {
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logger.warn("Executing testHardClipByReferenceCoordinates");
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@ -178,8 +168,8 @@ public class ReadClipperUnitTest extends BaseTest {
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Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader()));
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List<testParameter> testList = new LinkedList<testParameter>();
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testList.add(new testParameter(1,-1,1,4,"1H3M"));//clip 1 base at start
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testList.add(new testParameter(2,-1,2,4,"2H2M"));//clip 2 bases at start
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testList.add(new testParameter(1, -1, 1, 4, "1H3M"));//clip 1 base at start
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testList.add(new testParameter(2, -1, 2, 4, "2H2M"));//clip 2 bases at start
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for ( testParameter p : testList ) {
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init();
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@ -201,8 +191,8 @@ public class ReadClipperUnitTest extends BaseTest {
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Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader()));
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List<testParameter> testList = new LinkedList<testParameter>();
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testList.add(new testParameter(-1,4,0,3,"3M1H"));//clip 1 base at end
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testList.add(new testParameter(-1,3,0,2,"2M2H"));//clip 2 bases at end
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testList.add(new testParameter(-1, 4, 0, 3, "3M1H"));//clip 1 base at end
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testList.add(new testParameter(-1, 3, 0, 2, "2M2H"));//clip 2 bases at end
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for ( testParameter p : testList ) {
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init();
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@ -215,45 +205,55 @@ public class ReadClipperUnitTest extends BaseTest {
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}
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@Test ( enabled = false ) // TODO This function is returning null reads
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@Test ( enabled = true ) // TODO This function is returning null reads
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public void testHardClipLowQualEnds() {
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init();
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logger.warn("Executing testHardClipByReferenceCoordinates");
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logger.warn("Executing testHardClipByReferenceCoordinates");
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//Clip whole read
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Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new GATKSAMRecord(read.getHeader()));
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//clip 1 base at start
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expected = readClipper.hardClipLowQualEnds((byte)34);
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logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString());
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Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4));
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Assert.assertEquals(expected.getCigarString(), "1H3M");
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//clip 2 bases at start
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expected = readClipper.hardClipLowQualEnds((byte)44);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4));
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Assert.assertEquals(expected.getCigarString(), "2H2M");
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List<testParameter> testList = new LinkedList<testParameter>();
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testList.add(new testParameter(1,-1,1,4,"1H3M"));//clip 1 base at start
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testList.add(new testParameter(11,-1,2,4,"2H2M"));//clip 2 bases at start
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for ( testParameter p : testList ) {
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init();
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//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
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testIfEqual( readClipper.hardClipLowQualEnds( (byte)p.inputStart ),
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BASES.substring(p.substringStart,p.substringStop).getBytes(),
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QUALS.substring(p.substringStart,p.substringStop),
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p.cigar );
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}
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/* todo find a better way to test lowqual tail clipping on both sides
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// Reverse Quals sequence
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//readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
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readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
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//clip 1 base at end
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expected = readClipper.hardClipLowQualEnds((byte)'!');
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logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString());
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Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3));
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Assert.assertEquals(expected.getCigarString(), "3M1H");
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testList = new LinkedList<testParameter>();
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testList.add(new testParameter(1,-1,0,3,"3M1H"));//clip 1 base at end
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testList.add(new testParameter(11,-1,0,2,"2M2H"));//clip 2 bases at end
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//clip 2 bases at end
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expected = readClipper.hardClipLowQualEnds((byte)44);
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Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes());
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Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2));
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Assert.assertEquals(expected.getCigarString(), "2M2H");
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for ( testParameter p : testList ) {
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init();
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readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33
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//logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar);
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testIfEqual( readClipper.hardClipLowQualEnds( (byte)p.inputStart ),
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BASES.substring(p.substringStart,p.substringStop).getBytes(),
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QUALS.substring(p.substringStart,p.substringStop),
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p.cigar );
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}
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*/
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}
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// revert Qual sequence
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readClipper.getRead().setBaseQualityString(QUALS);
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public class CigarReadMaker {
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}
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@Test ( enabled = false )
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public void testHardClipSoftClippedBases() {
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// Generate a list of cigars to test
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// We will use testParameter in the following way
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// Right tail, left tail,
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}
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}
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