From 4fd5630f6a65c75eaf1a80facfc55cb86b42c390 Mon Sep 17 00:00:00 2001 From: Roger Zurawicki Date: Wed, 28 Sep 2011 23:13:50 -0400 Subject: [PATCH] Added ReadClipper Unit Test * Includes tests that include HardClip to Read and Reference Coords. * Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing --- .../sting/utils/clipreads/ReadClipper.java | 2 +- .../utils/clipreads/ReadClipperUnitTest.java | 225 ++++++++++++++++++ 2 files changed, 226 insertions(+), 1 deletion(-) create mode 100644 public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java index 83db20238..4c07f15f6 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java @@ -68,7 +68,7 @@ public class ReadClipper { return result; } - private SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) { + protected SAMRecord hardClipByReferenceCoordinates(int refStart, int refStop) { int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart, ReadUtils.ClippingTail.RIGHT_TAIL); int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop, ReadUtils.ClippingTail.LEFT_TAIL); diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java new file mode 100644 index 000000000..1415379db --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java @@ -0,0 +1,225 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.clipreads; + +import net.sf.samtools.*; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.util.LinkedList; +import java.util.List; + +/** + * Created by IntelliJ IDEA. + * User: roger + * Date: 9/28/11 + * Time: 9:54 PM + * To change this template use File | Settings | File Templates. + */ +public class ReadClipperUnitTest extends BaseTest { + + // TODO: Add error messages on failed tests + + SAMRecord read, expected; + ReadClipper readClipper; + final static String BASES = "ACTG"; + final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63 + + @BeforeClass + public void init() { + SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000); + read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length()); + read.setReadUnmappedFlag(true); + read.setReadBases(new String(BASES).getBytes()); + read.setBaseQualityString(new String(QUALS)); + + readClipper = new ReadClipper(read); + } + + @Test + public void testHardClipBothEndsByReferenceCoordinates() { + logger.warn("Executing testHardClipBothEndsByReferenceCoordinates"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(0,0), new SAMRecord(read.getHeader())); + //clip 1 base + expected = readClipper.hardClipBothEndsByReferenceCoordinates(0,3); + Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes()); + Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3)); + Assert.assertEquals(expected.getCigarString(), "1H2M1H"); + + } + + @Test + public void testHardClipByReadCoordinates() { + logger.warn("Executing testHardClipByReadCoordinates"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipByReadCoordinates(0,3), new SAMRecord(read.getHeader())); + + //clip 1 base at start + 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"); + + } + + @Test + public void testHardClipByReferenceCoordinates() { + logger.warn("Executing testHardClipByReferenceCoordinates"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipByReferenceCoordinates(1,4), new SAMRecord(read.getHeader())); + + //clip 1 base at start + expected = readClipper.hardClipByReferenceCoordinates(-1,1); + 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.hardClipByReferenceCoordinates(3,-1); + 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.hardClipByReferenceCoordinates(-1,2); + 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.hardClipByReferenceCoordinates(2,-1); + Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes()); + Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2)); + Assert.assertEquals(expected.getCigarString(), "2M2H"); + + } + + @Test + public void testHardClipByReferenceCoordinatesLeftTail() { + logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesLeftTail(4), new SAMRecord(read.getHeader())); + + //clip 1 base at start + expected = readClipper.hardClipByReferenceCoordinatesLeftTail(1); + 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.hardClipByReferenceCoordinatesLeftTail(2); + Assert.assertEquals(expected.getReadBases(), BASES.substring(2,4).getBytes()); + Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(2,4)); + Assert.assertEquals(expected.getCigarString(), "2H2M"); + + } + + @Test + public void testHardClipByReferenceCoordinatesRightTail() { + logger.warn("Executing testHardClipByReferenceCoordinatesRightTail"); + + //Clip whole read + Assert.assertEquals(readClipper.hardClipByReferenceCoordinatesRightTail(1), new SAMRecord(read.getHeader())); + + //clip 1 base at end + expected = readClipper.hardClipByReferenceCoordinatesRightTail(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 end + expected = readClipper.hardClipByReferenceCoordinatesRightTail(2); + Assert.assertEquals(expected.getReadBases(), BASES.substring(0,2).getBytes()); + Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(0,2)); + Assert.assertEquals(expected.getCigarString(), "2M2H"); + + } + + @Test + public void testHardClipLowQualEnds() { + logger.warn("Executing testHardClipByReferenceCoordinates"); + + + //Clip whole read + Assert.assertEquals(readClipper.hardClipLowQualEnds((byte)64), new SAMRecord(read.getHeader())); + + //clip 1 base at start + expected = readClipper.hardClipLowQualEnds((byte)34); + 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"); + + // Reverse Quals sequence + readClipper.getRead().setBaseQualityString("?5+!"); // 63,53,43,33 + + //clip 1 base at end + expected = readClipper.hardClipLowQualEnds((byte)34); + 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 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"); + + // revert Qual sequence + readClipper.getRead().setBaseQualityString(QUALS); + } +}