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>

public/java/test/org/broadinstitute/sting/utils/clipreads/CigarStringTestPair.java

@@ -0,0 +1,18 @@
+package org.broadinstitute.sting.utils.clipreads;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: roger
+ * Date: 11/29/11
+ * Time: 4:53 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class CigarStringTestPair {
+    public String toTest;
+    public String expected;
+
+    public CigarStringTestPair(String ToTest, String Expected) {
+        this.toTest = ToTest;
+        this.expected = Expected;
+    }
+}

public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java

@@ -0,0 +1,185 @@
+package org.broadinstitute.sting.utils.clipreads;
+
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.TextCigarCodec;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+
+import java.util.*;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: roger
+ * Date: 11/27/11
+ * Time: 6:45 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ClipReadsTestUtils {
+    //Should contain all the utils needed for tests to mass produce
+    //reads, cigars, and other needed classes
+
+    final static String BASES = "ACTG";
+    final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
+
+    public static void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) {
+        // Because quals to char start at 33 for visibility
+        baseQuals = subtractToArray(baseQuals, 33);
+
+        Assert.assertEquals(read.getReadBases(), readBases);
+        Assert.assertEquals(read.getBaseQualities(), baseQuals);
+        Assert.assertEquals(read.getCigarString(), cigar);
+    }
+
+    public static void testCigar(GATKSAMRecord read, String cigar) {
+        Assert.assertEquals(read.getCigarString(), cigar);
+    }
+
+    public static void testBaseQual(GATKSAMRecord read, byte[] readBases, byte[] baseQuals) {
+        // Because quals to chars start at 33 for visibility
+        baseQuals = subtractToArray(baseQuals, 33);
+
+        if (readBases.length > 0 && baseQuals.length > 0) {
+            Assert.assertEquals(read.getReadBases(), readBases);
+            Assert.assertEquals(read.getBaseQualities(), baseQuals);
+        } else
+            Assert.assertTrue(read.isEmpty());
+    }
+
+    private static byte[] subtractToArray(byte[] array, int n) {
+        if (array == null)
+            return null;
+
+        byte[] output = new byte[array.length];
+
+        for (int i = 0; i < array.length; i++)
+            output[i] = (byte) (array[i] - n);
+
+        return output;
+    }
+
+    // What the test read looks like
+    // Ref:    10 11 12 13 14 15 16 17
+    // Read:   0  1  2  3  -  -  -  -
+    // --------------------------------
+    // Bases:  A  C  T  G  -  -  -  -
+    // Quals:  !  +  5  ?  -  -  -  -
+
+    public static GATKSAMRecord makeRead() {
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
+        GATKSAMRecord output = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, BASES.length());
+        output.setReadBases(new String(BASES).getBytes());
+        output.setBaseQualityString(new String(QUALS));
+
+        return output;
+    }
+
+    public static GATKSAMRecord makeReadFromCigar(Cigar cigar) {
+
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
+        GATKSAMRecord output = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, cigar.getReadLength());
+        output.setReadBases(cycleString(BASES, cigar.getReadLength()).getBytes());
+        output.setBaseQualityString(cycleString(QUALS, cigar.getReadLength()));
+        output.setCigar(cigar);
+
+        return output;
+    }
+
+    private static 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;
+    }
+
+    public static 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> indelOptions1 = new LinkedList<Cigar>();
+        indelOptions1.add(new Cigar());
+        //indelOptions1.add( TextCigarCodec.getSingleton().decode("1I1D"));
+        //indelOptions1.add( TextCigarCodec.getSingleton().decode("1D1I") );
+        indelOptions1.add(TextCigarCodec.getSingleton().decode("1I"));
+        indelOptions1.add(TextCigarCodec.getSingleton().decode("1D"));
+
+        LinkedList<Cigar> indelOptions2 = new LinkedList<Cigar>();
+        indelOptions2.add(new Cigar());
+        indelOptions2.add(TextCigarCodec.getSingleton().decode("1I"));
+        indelOptions2.add(null);
+
+
+        // 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 : indelOptions1) {
+                for (Cigar indelEnd : indelOptions2) {
+                    for (Cigar clipStart : clippingOptionsStart) {
+                        for (Cigar clipEnd : clippingOptionsEnd) {
+                            // Create a list of Cigar Elements and construct Cigar
+                            List<CigarElement> CigarBuilder = new ArrayList<CigarElement>();
+                            // add starting clipping (H/S)
+                            CigarBuilder.addAll(clipStart.getCigarElements());
+                            // add first base (M)
+                            CigarBuilder.addAll(Base.getCigarElements());
+                            // add first indel
+                            CigarBuilder.addAll(indelStart.getCigarElements());
+                            // add second base (M)
+                            CigarBuilder.addAll(Base.getCigarElements());
+                            // add another indel or nothing (M)
+                            if (indelEnd != null)
+                                CigarBuilder.addAll(indelEnd.getCigarElements());
+                            // add final clipping (S/H)
+                            CigarBuilder.addAll(clipEnd.getCigarElements());
+
+
+                            output.add(new Cigar(removeConsecutiveElements(CigarBuilder)));
+
+                        }
+                    }
+                }
+            }
+        }
+
+        return output;
+    }
+
+    private static 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;
+    }
+}

public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java

@@ -0,0 +1,69 @@
+package org.broadinstitute.sting.utils.clipreads;
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import java.util.LinkedList;
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: roger
+ * Date: 11/27/11
+ * Time: 5:17 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public class ClippingOpUnitTest extends BaseTest {
+
+    ClippingOp clippingOp;
+    GATKSAMRecord read;
+
+    @BeforeTest
+    public void init() {
+        read = ClipReadsTestUtils.makeRead();
+    }
+
+    @Test
+    private void testHardClip() {
+        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
+        testList.add(new TestParameter(0, 2, 3, 4, "3H1M"));//clip 3 bases at start
+        testList.add(new TestParameter(1, 3, 0, 1, "1M3H"));//clip 3 bases at end
+
+        for (TestParameter p : testList) {
+            init();
+            clippingOp = new ClippingOp(p.inputStart, p.inputStop);
+            logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.substringStart + "," + p.substringStop + "," + p.cigar);
+            ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.HARDCLIP_BASES, read),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.QUALS.substring(p.substringStart, p.substringStop).getBytes(),
+                    p.cigar);
+        }
+
+    }
+
+    @Test
+    private void testSoftClip() {
+        List<TestParameter> testList = new LinkedList<TestParameter>();
+        testList.add(new TestParameter(0, 0, -1, -1, "1S3M"));//clip 1 base at start
+        testList.add(new TestParameter(3, 3, -1, -1, "3M1S"));//clip 1 base at end
+        testList.add(new TestParameter(0, 1, -1, -1, "2S2M"));//clip 2 bases at start
+        testList.add(new TestParameter(2, 3, -1, -1, "2M2S"));//clip 2 bases at end
+        testList.add(new TestParameter(0, 2, -1, -1, "3S1M"));//clip 3 bases at start
+        testList.add(new TestParameter(1, 3, -1, -1, "1M3S"));//clip 3 bases at end
+
+        for (TestParameter p : testList) {
+            init();
+            clippingOp = new ClippingOp(p.inputStart, p.inputStop);
+            logger.warn("Testing Parameters: " + p.inputStart + "," + p.inputStop + "," + p.cigar);
+            ClipReadsTestUtils.testBaseQualCigar(clippingOp.apply(ClippingRepresentation.SOFTCLIP_BASES, read),
+                    ClipReadsTestUtils.BASES.getBytes(), ClipReadsTestUtils.QUALS.getBytes(), p.cigar);
+        }
+
+    }
+}

public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java

@@ -25,16 +25,19 @@
 
 package org.broadinstitute.sting.utils.clipreads;
 
-import net.sf.samtools.*;
+import net.sf.samtools.Cigar;
+import net.sf.samtools.CigarElement;
+import net.sf.samtools.CigarOperator;
+import net.sf.samtools.TextCigarCodec;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import java.util.*;
+import java.util.LinkedList;
+import java.util.List;
 
 /**
  * Created by IntelliJ IDEA.
@@ -47,209 +50,202 @@ public class ReadClipperUnitTest extends BaseTest {
 
     // TODO: exception testing, make cases that should fail will fail
 
-    //int debug = 0;
+    // TODO: add indels to all test cases
 
-    GATKSAMRecord read, expected;
     ReadClipper readClipper;
-    final static String BASES = "ACTG";
-    final static String QUALS = "!+5?"; //ASCII values = 33,43,53,63
-
-    private void testBaseQualCigar(GATKSAMRecord read, byte[] readBases, byte[] baseQuals, String cigar) {
-        // Because quals to char start at 33 for visibility
-        baseQuals = subtractToArray(baseQuals, 33);
-
-        Assert.assertEquals(read.getReadBases(), readBases);
-        Assert.assertEquals(read.getBaseQualities(), baseQuals);
-        Assert.assertEquals(read.getCigarString(), cigar);
-    }
-
-    private void testBaseQual(GATKSAMRecord read, byte[] readBases, byte[] baseQuals) {
-        // Because quals to chars start at 33 for visibility
-        baseQuals = subtractToArray(baseQuals, 33);
-
-        if ( readBases.length > 0 && baseQuals.length > 0 ) {
-            Assert.assertEquals(read.getReadBases(), readBases);
-            Assert.assertEquals(read.getBaseQualities(), baseQuals);
-        }
-        else
-            Assert.assertTrue(read.isEmpty());
-    }
-
-    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;
-            }
-    }
-
-    private byte[] subtractToArray (byte[] array, int n ) {
-        if ( array == null)
-            return null;
-
-        byte[] output = new byte[array.length];
-
-        for ( int i = 0; i < array.length; i++)
-            output[i] = (byte) ( array[i] - n );
-
-        return output;
-    }
-
-    // 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);
+        readClipper = new ReadClipper(ClipReadsTestUtils.makeRead());
-        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 )
+    @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()));
+        Assert.assertEquals(readClipper.hardClipBothEndsByReferenceCoordinates(10, 10), new GATKSAMRecord(readClipper.read.getHeader()));
 
         //clip 1 base
-        expected = readClipper.hardClipBothEndsByReferenceCoordinates(1,4);
+        ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipBothEndsByReferenceCoordinates(10, 13),
-        Assert.assertEquals(expected.getReadBases(), BASES.substring(1,3).getBytes());
+                ClipReadsTestUtils.BASES.substring(1, 3).getBytes(), ClipReadsTestUtils.QUALS.substring(1, 3).getBytes(),
-        Assert.assertEquals(expected.getBaseQualityString(), QUALS.substring(1,3));
+                "1H2M1H");
-        Assert.assertEquals(expected.getCigarString(), "1H2M1H");
 
+        List<CigarStringTestPair> cigarStringTestPairs = new LinkedList<CigarStringTestPair>();
+        cigarStringTestPairs.add(new CigarStringTestPair("5M1D1M2I4M5I6M1D3M2I100M", "1H4M1D1M2I4M5I6M1D3M2I99M1H"));
+        //cigarStringTestPairs.add( new CigarStringTestPair("5M1I1M2I1M","1H4M1I1M2I1H"));
+        cigarStringTestPairs.add(new CigarStringTestPair("1S1M1I1M1I1M1I1M1I1M1I1M1S", "1H1M1I1M1I1M1I1M1I1M1I1M1H"));
+        cigarStringTestPairs.add(new CigarStringTestPair("1S1M1D1M1D1M1D1M1D1M1D1M1S", "1H1M1D1M1D1M1D1M1D1M1D1M1H"));
+
+        for (CigarStringTestPair pair : cigarStringTestPairs) {
+            readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar(TextCigarCodec.getSingleton().decode(pair.toTest)));
+            ClipReadsTestUtils.testCigar(readClipper.hardClipBothEndsByReferenceCoordinates(
+                    ReadUtils.getRefCoordSoftUnclippedStart(readClipper.read),
+                    ReadUtils.getRefCoordSoftUnclippedEnd(readClipper.read)),
+                    pair.expected);
+        }
+        /*
+        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>();
+        List<TestParameter> testList = new LinkedList<TestParameter>();
-        testList.add(new testParameter(0,0,1,4,"1H3M"));//clip 1 base at start
+        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(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(0, 1, 2, 4, "2H2M"));//clip 2 bases at start
-        testList.add(new testParameter(2,3,0,2,"2M2H"));//clip 2 bases at end
+        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),
+            ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReadCoordinates(p.inputStart, p.inputStop),
-                    BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-                    QUALS.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>();
+        List<TestParameter> testList = new LinkedList<TestParameter>();
-        testList.add(new testParameter(-1,1,1,4,"1H3M"));//clip 1 base at start
+        testList.add(new TestParameter(-1, 10, 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(13, -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(-1, 11, 2, 4, "2H2M"));//clip 2 bases at start
-        testList.add(new testParameter(3,-1,0,2,"2M2H"));//clip 2 bases at end
+        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),
+            ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinates(p.inputStart, p.inputStop),
-                    BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-                    QUALS.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>();
+        List<TestParameter> testList = new LinkedList<TestParameter>();
-        testList.add(new testParameter(1, -1, 1, 4, "1H3M"));//clip 1 base at start
+        testList.add(new TestParameter(10, -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(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),
+            ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesLeftTail(p.inputStart),
-                    BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-                    QUALS.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>();
+        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, 13, 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, 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),
+            ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipByReferenceCoordinatesRightTail(p.inputStop),
-                    BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-                    QUALS.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>();
+        List<TestParameter> testList = new LinkedList<TestParameter>();
-        testList.add(new testParameter(1,-1,1,4,"1H3M"));//clip 1 base at start
+        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
+        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),
+            ClipReadsTestUtils.testBaseQualCigar(readClipper.hardClipLowQualEnds((byte) p.inputStart),
-                    BASES.substring(p.substringStart, p.substringStop).getBytes(),
+                    ClipReadsTestUtils.BASES.substring(p.substringStart, p.substringStop).getBytes(),
-                    QUALS.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
@@ -272,127 +268,13 @@ public class ReadClipperUnitTest extends BaseTest {
         */
     }
 
-  //  public class ReadMaker  {
+    @Test(enabled = true)
-    //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 )
     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 );
+            readClipper = new ReadClipper(ClipReadsTestUtils.makeReadFromCigar(cigar));
-
-
-            try {
-                readClipper.hardClipLeadingInsertions();
-            }
-            catch ( ReviewedStingException e ) {}
-
 
             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 ) {
+            else if (cigarElements.get(0).getOperator() == CigarOperator.INSERTION) {
                 expectEmptyRead = true;
             }
 
-            if ( cigarElements.get(CigarListLength - 1).getOperator() == CigarOperator.HARD_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 )
+                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)
-            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 ),
+                    cigar.toString(), readBases.substring(clipStart, readBases.length() - clipEnd),
-                    baseQuals.substring( clipStart, baseQuals.length() - clipEnd ) ) );
+                    baseQuals.substring(clipStart, baseQuals.length() - clipEnd)));
             //if (expectEmptyRead)
             //    testBaseQual( readClipper.hardClipSoftClippedBases(), new byte[0], new byte[0] );
             //else
-                testBaseQual(readClipper.hardClipSoftClippedBases(),
+            ClipReadsTestUtils.testBaseQual(readClipper.hardClipSoftClippedBases(),
-                    readBases.substring( clipStart, readBases.length() - clipEnd ).getBytes(),
+                    readBases.substring(clipStart, readBases.length() - clipEnd).getBytes(),
-                    baseQuals.substring( clipStart, baseQuals.length() - clipEnd ).getBytes());
+                    baseQuals.substring(clipStart, baseQuals.length() - clipEnd).getBytes());
-            logger.warn("Cigar: "+cigar.toString()+" PASSED!");
+            logger.warn("Cigar: " + cigar.toString() + " PASSED!");
         }
         // We will use testParameter in the following way
         // Right tail, left tail,

public/java/test/org/broadinstitute/sting/utils/clipreads/TestParameter.java

@@ -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;
+    }
+}