From 5b678e3b94a086c40a8cd7baf18dba713d07fe50 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sun, 18 Dec 2011 12:26:06 -0500
Subject: [PATCH] Remove ClippingOp UnitTests

* all testing functionality is in the ReadClipperUnitTest, no need to double test.
* class and package naming cleanup
---
 .../sting/gatk/walkers/ClipReadsWalker.java   |  6 +-
 .../{clipreads => clipping}/ClippingOp.java   |  2 +-
 .../ClippingRepresentation.java               |  2 +-
 .../{clipreads => clipping}/ReadClipper.java  |  2 +-
 .../ReadClipperTestUtils.java}                |  8 ++-
 .../ReadClipperUnitTest.java                  | 24 +++----
 .../utils/clipreads/ClippingOpUnitTest.java   | 67 -------------------
 7 files changed, 23 insertions(+), 88 deletions(-)
 rename public/java/src/org/broadinstitute/sting/utils/{clipreads => clipping}/ClippingOp.java (99%)
 rename public/java/src/org/broadinstitute/sting/utils/{clipreads => clipping}/ClippingRepresentation.java (95%)
 rename public/java/src/org/broadinstitute/sting/utils/{clipreads => clipping}/ReadClipper.java (99%)
 rename public/java/test/org/broadinstitute/sting/utils/{clipreads/ClipReadsTestUtils.java => clipping/ReadClipperTestUtils.java} (98%)
 rename public/java/test/org/broadinstitute/sting/utils/{clipreads => clipping}/ReadClipperUnitTest.java (94%)
 delete mode 100644 public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
index d1148cbd5..ff3867120 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
@@ -38,9 +38,9 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.clipreads.ClippingOp;
-import org.broadinstitute.sting.utils.clipreads.ClippingRepresentation;
-import org.broadinstitute.sting.utils.clipreads.ReadClipper;
+import org.broadinstitute.sting.utils.clipping.ClippingOp;
+import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
+import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
rename to public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
index 0bb8c3e6f..f440eda5d 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import com.google.java.contract.Requires;
 import net.sf.samtools.Cigar;
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java
rename to public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
index d574ba2f0..c9d8730d1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ClippingRepresentation.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 /**
  * How should we represent a clipped bases in a read?
diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
rename to public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
index e6b3ce929..6e3f37980 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import com.google.java.contract.Requires;
 import net.sf.samtools.CigarElement;
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java
similarity index 98%
rename from public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
rename to public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java
index 048d9d8e0..18108e0a1 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClipReadsTestUtils.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
@@ -8,7 +8,9 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 
-import java.util.*;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Stack;
 
 /**
  * Created by IntelliJ IDEA.
@@ -17,7 +19,7 @@ import java.util.*;
  * Time: 6:45 AM
  * To change this template use File | Settings | File Templates.
  */
-public class ClipReadsTestUtils {
+public class ReadClipperTestUtils {
     //Should contain all the utils needed for tests to mass produce
     //reads, cigars, and other needed classes
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
similarity index 94%
rename from public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
rename to public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
index fcde5f360..3b4b0abce 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.clipreads;
+package org.broadinstitute.sting.utils.clipping;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
@@ -50,13 +50,13 @@ public class ReadClipperUnitTest extends BaseTest {
 
     @BeforeClass
     public void init() {
-        cigarList = ClipReadsTestUtils.generateCigarList(maximumCigarSize);
+        cigarList = ReadClipperTestUtils.generateCigarList(maximumCigarSize);
     }
 
     @Test(enabled = true)
     public void testHardClipBothEndsByReferenceCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             int readLength = alnStart - alnEnd;
@@ -71,7 +71,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReadCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int readLength = read.getReadLength();
             for (int i=0; i<readLength; i++) {
                 GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReadCoordinates(0, i);
@@ -86,7 +86,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinates() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             for (int i=alnStart; i<=alnEnd; i++) {
@@ -108,7 +108,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinatesLeftTail() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             if (ReadUtils.getRefCoordSoftUnclippedStart(read) == alnStart) {                                // we can't test left clipping if the read has hanging soft clips on the left side
@@ -124,7 +124,7 @@ public class ReadClipperUnitTest extends BaseTest {
     @Test(enabled = true)
     public void testHardClipByReferenceCoordinatesRightTail() {
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int alnStart = read.getAlignmentStart();
             int alnEnd = read.getAlignmentEnd();
             if (ReadUtils.getRefCoordSoftUnclippedEnd(read) == alnEnd) {                                        // we can't test right clipping if the read has hanging soft clips on the right side
@@ -144,7 +144,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
         // create a read for every cigar permutation
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             int readLength = read.getReadLength();
             byte [] quals = new byte[readLength];
 
@@ -216,7 +216,7 @@ public class ReadClipperUnitTest extends BaseTest {
         GATKSAMRecord expected = ArtificialSAMUtils.createArtificialRead(CLIPPED_BASES, CLIPPED_QUALS, CLIPPED_CIGAR);
 
         ReadClipper lowQualClipper = new ReadClipper(read);
-        ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
+        ReadClipperTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
     }
 
     @Test(enabled = true)
@@ -224,7 +224,7 @@ public class ReadClipperUnitTest extends BaseTest {
 
         // Generate a list of cigars to test
         for (Cigar cigar : cigarList) {
-            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
             ReadClipper readClipper = new ReadClipper(read);
             GATKSAMRecord clippedRead = readClipper.hardClipSoftClippedBases();
 
@@ -276,12 +276,12 @@ public class ReadClipperUnitTest extends BaseTest {
     public void testHardClipLeadingInsertions() {
         for (Cigar cigar : cigarList) {
             if (startsWithInsertion(cigar)) {
-                GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+                GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar);
                 GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipLeadingInsertions();
 
                 int expectedLength = read.getReadLength() - leadingInsertionLength(read.getCigar());
                 if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
-                    expectedLength -= leadingInsertionLength(ClipReadsTestUtils.invertCigar(read.getCigar()));
+                    expectedLength -= leadingInsertionLength(ReadClipperTestUtils.invertCigar(read.getCigar()));
 
                 if (! clippedRead.isEmpty()) {
                     Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString()));  // check that everything else is still there
diff --git a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java
deleted file mode 100644
index dd674ff1c..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ClippingOpUnitTest.java
+++ /dev/null
@@ -1,67 +0,0 @@
-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;
-
-
-/**
- * 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);
-//        }
-
-    }
-}