From 284430d61dafcdf47177040bbf416b7501e47168 Mon Sep 17 00:00:00 2001 From: Roger Zurawicki Date: Tue, 15 Nov 2011 00:13:52 -0500 Subject: [PATCH] Added more basic UnitTests for ReadClipper hardClipByReadCoordinatesWorks hardClipLowQualTailsWorks --- .../utils/clipreads/ReadClipperUnitTest.java | 206 +++++++++--------- 1 file changed, 103 insertions(+), 103 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java index 0c71a845e..ecb5a6d33 100644 --- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java @@ -30,8 +30,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.testng.Assert; -import org.testng.annotations.BeforeTest; -import org.testng.annotations.Test; +import org.testng.annotations.*; import java.util.LinkedList; import java.util.List; @@ -47,7 +46,6 @@ public class ReadClipperUnitTest extends BaseTest { // TODO: Add error messages on failed tests - //int debug = 0; GATKSAMRecord read, expected; @@ -55,73 +53,6 @@ public class ReadClipperUnitTest extends BaseTest { final static String BASES = "ACTG"; final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63 - // What the test read looks like - // Ref: 1 2 3 4 5 6 7 8 - // Read: 0 1 2 3 - - - - - // ----------------------------- - // Bases: A C T G - - - - - // Quals: ! + 5 ? - - - - - - @BeforeTest - public void init() { - SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); - read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length()); - read.setReadBases(new String(BASES).getBytes()); - read.setBaseQualityString(new String(QUALS)); - - readClipper = new ReadClipper(read); - //logger.warn(read.getCigarString()); - } - - @Test ( enabled = true ) - public void testHardClipBothEndsByReferenceCoordinates() { - init(); - logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); - //int debug = 1; - //Clip whole read - Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(1,1), new GATKSAMRecord(read.getHeader())); - //clip 1 base - expected = readClipper.hardClipBothEndsByReferenceCoordinates(1,4); - Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3)); - Assert.assertEquals(expected.getCigarString(), "1H2M1H"); - - } - - @Test ( enabled = false ) // TODO This fails at hardClipCigar and returns a NullPointerException - public void testHardClipByReadCoordinates() { - init(); - logger.warn("Executing testHardClipByReadCoordinates"); - - //Clip whole read - Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader())); - - //clip 1 base at start - System.out.println(readClipper.read.getCigarString()); - expected = readClipper.hardClipByReadCoordinates(0,0); - Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4)); - Assert.assertEquals(expected.getCigarString(), "1H3M"); - - //clip 1 base at end - expected = readClipper.hardClipByReadCoordinates(3,3); - Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3)); - Assert.assertEquals(expected.getCigarString(), "3M1H"); - - //clip 2 bases at start - expected = readClipper.hardClipByReadCoordinates(0,1); - Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4)); - Assert.assertEquals(expected.getCigarString(), "2H2M"); - - //clip 2 bases at end - expected = readClipper.hardClipByReadCoordinates(2,3); - Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2)); - Assert.assertEquals(expected.getCigarString(), "2M2H"); - - } public void testIfEqual( GATKSAMRecord read, byte[] readBases, String baseQuals, String cigar) { Assert.assertEquals(read.getReadBases(), readBases); @@ -145,6 +76,65 @@ public class ReadClipperUnitTest extends BaseTest { } } + // What the test read looks like + // Ref: 1 2 3 4 5 6 7 8 + // Read: 0 1 2 3 - - - - + // ----------------------------- + // Bases: A C T G - - - - + // Quals: ! + 5 ? - - - - + + @BeforeMethod + public void init() { + SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); + read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length()); + read.setReadBases(new String(BASES).getBytes()); + read.setBaseQualityString(new String(QUALS)); + + readClipper = new ReadClipper(read); + //logger.warn(read.getCigarString()); + } + + @Test ( enabled = true ) + public void testHardClipBothEndsByReferenceCoordinates() { + + logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); + //int debug = 1; + //Clip whole read + Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(1,1), new GATKSAMRecord(read.getHeader())); + + //clip 1 base + expected = readClipper.hardClipBothEndsByReferenceCoordinates(1,4); + Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes()); + Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3)); + Assert.assertEquals(expected.getCigarString(), "1H2M1H"); + + } + + @Test ( enabled = true ) + public void testHardClipByReadCoordinates() { + + logger.warn("Executing testHardClipByReadCoordinates"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new GATKSAMRecord(read.getHeader())); + + List testList = new LinkedList(); + 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 ) { + init(); + //logger.warn("Testing Parameters: " + p.inputStart+","+p.inputStop+","+p.substringStart+","+p.substringStop+","+p.cigar); + testIfEqual( readClipper.hardClipByReadCoordinates(p.inputStart, p.inputStop), + BASES.substring(p.substringStart,p.substringStop).getBytes(), + QUALS.substring(p.substringStart,p.substringStop), + p.cigar ); + } + + } + @Test ( enabled = true ) public void testHardClipByReferenceCoordinates() { logger.warn("Executing testHardClipByReferenceCoordinates"); @@ -178,8 +168,8 @@ public class ReadClipperUnitTest extends BaseTest { Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new GATKSAMRecord(read.getHeader())); List testList = new LinkedList(); - 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 + 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 for ( testParameter p : testList ) { init(); @@ -201,8 +191,8 @@ public class ReadClipperUnitTest extends BaseTest { Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new GATKSAMRecord(read.getHeader())); List testList = new LinkedList(); - 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 + 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 for ( testParameter p : testList ) { init(); @@ -215,45 +205,55 @@ public class ReadClipperUnitTest extends BaseTest { } - @Test ( enabled = false ) // TODO This function is returning null reads + @Test ( enabled = true ) // TODO This function is returning null reads public void testHardClipLowQualEnds() { - init(); - logger.warn("Executing testHardClipByReferenceCoordinates"); + logger.warn("Executing testHardClipByReferenceCoordinates"); //Clip whole read Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new GATKSAMRecord(read.getHeader())); - //clip 1 base at start - expected = readClipper.hardClipLowQualEnds((byte)34); - logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString()); - Assert.assertEquals(expected.getReadBases(), BASES.substring(1,4).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,4)); - Assert.assertEquals(expected.getCigarString(), "1H3M"); - - //clip 2 bases at start - expected = readClipper.hardClipLowQualEnds((byte)44); - Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4)); - Assert.assertEquals(expected.getCigarString(), "2H2M"); + List testList = new LinkedList(); + 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 ) { + init(); + //logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar); + testIfEqual( readClipper.hardClipLowQualEnds( (byte)p.inputStart ), + BASES.substring(p.substringStart,p.substringStop).getBytes(), + QUALS.substring(p.substringStart,p.substringStop), + p.cigar ); + } + /* todo find a better way to test lowqual tail clipping on both sides // Reverse Quals sequence - //readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33 + readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33 - //clip 1 base at end - expected = readClipper.hardClipLowQualEnds((byte)'!'); - logger.warn(expected.getBaseQualities().toString()+","+expected.getBaseQualityString()); - Assert.assertEquals(expected.getReadBases(), BASES.substring(0,3).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,3)); - Assert.assertEquals(expected.getCigarString(), "3M1H"); + testList = new LinkedList(); + testList.add(new testParameter(1,-1,0,3,"3M1H"));//clip 1 base at end + testList.add(new testParameter(11,-1,0,2,"2M2H"));//clip 2 bases at end - //clip 2 bases at end - expected = readClipper.hardClipLowQualEnds((byte)44); - Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes()); - Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2)); - Assert.assertEquals(expected.getCigarString(), "2M2H"); + for ( testParameter p : testList ) { + init(); + readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33 + //logger.warn("Testing Parameters: " + p.inputStart+","+p.substringStart+","+p.substringStop+","+p.cigar); + testIfEqual( readClipper.hardClipLowQualEnds( (byte)p.inputStart ), + BASES.substring(p.substringStart,p.substringStop).getBytes(), + QUALS.substring(p.substringStart,p.substringStop), + p.cigar ); + } + */ + } - // revert Qual sequence - readClipper.getRead().setBaseQualityString(QUALS); + public class CigarReadMaker { + + } + + @Test ( enabled = false ) + public void testHardClipSoftClippedBases() { + + // Generate a list of cigars to test + // We will use testParameter in the following way + // Right tail, left tail, } } \ No newline at end of file