Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/carneiro/gatk/RR into rr

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);
 

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);
+    }
+}