From c26295919e6cfb4903c11ea0646d2c93039de4d9 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 16 Dec 2011 14:36:27 -0500
Subject: [PATCH] Added hardClipBothEndsByReferenceCoordinates UnitTest for the
 ReadClipper

---
 .../utils/clipreads/ReadClipperUnitTest.java  | 47 ++++++++++---------
 1 file changed, 26 insertions(+), 21 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 fc1459ee0..2e2b5f373 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
@@ -34,7 +34,6 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import java.util.List;
@@ -48,10 +47,6 @@ import java.util.List;
  */
 public class ReadClipperUnitTest extends BaseTest {
 
-    // TODO: exception testing, make cases that should fail will fail
-
-    // TODO: add indels to all test cases
-
     List<Cigar> cigarList;
     int maximumCigarSize = 10;
 
@@ -64,6 +59,18 @@ public class ReadClipperUnitTest extends BaseTest {
     public void testHardClipBothEndsByReferenceCoordinates() {
         logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
 
+        for (Cigar cigar : cigarList) {
+            GATKSAMRecord read = ClipReadsTestUtils.makeReadFromCigar(cigar);
+            int alnStart = read.getAlignmentStart();
+            int alnEnd = read.getAlignmentEnd();
+            int readLength = alnStart - alnEnd;
+            for (int i=0; i<readLength/2; i++) {
+                GATKSAMRecord clippedRead = (new ReadClipper(read)).hardClipBothEndsByReferenceCoordinates(alnStart + i, alnEnd - i);
+                Assert.assertTrue(clippedRead.getAlignmentStart() >= alnStart + i, String.format("Clipped alignment start is less than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
+                Assert.assertTrue(clippedRead.getAlignmentEnd() <= alnEnd + i, String.format("Clipped alignment end is greater than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
+            }
+        }
+
     }
 
     @Test(enabled = true)
@@ -116,7 +123,7 @@ public class ReadClipperUnitTest extends BaseTest {
                 // Tests
 
                 // Make sure the low qualities are gone
-                testNoLowQualBases(clipLeft,  LOW_QUAL);
+                assertNoLowQualBases(clipLeft, LOW_QUAL);
 
                 // Can't run this test with the current contract of no hanging insertions
                 //Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
@@ -131,7 +138,7 @@ public class ReadClipperUnitTest extends BaseTest {
                 // Tests
 
                 // Make sure the low qualities are gone
-                testNoLowQualBases(clipRight, LOW_QUAL);
+                assertNoLowQualBases(clipRight, LOW_QUAL);
 
                 // Make sure we haven't clipped any high quals -- Can't run this test with the current contract of no hanging insertions
                 //Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipRight.getReadLength(), readLength - nLowQualBases, read.getCigarString(), clipRight.getCigarString()));
@@ -149,7 +156,7 @@ public class ReadClipperUnitTest extends BaseTest {
                     // Tests
 
                     // Make sure the low qualities are gone
-                    testNoLowQualBases(clipBoth,  LOW_QUAL);
+                    assertNoLowQualBases(clipBoth, LOW_QUAL);
 
                     // Can't run this test with the current contract of no hanging insertions
                     //Assert.assertEquals(clipLeft.getReadLength(), readLength - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipRight.getReadLength(), readLength - (2*nLowQualBases), read.getCigarString(), clipBoth.getCigarString()));
@@ -158,11 +165,7 @@ public class ReadClipperUnitTest extends BaseTest {
 //            logger.warn(String.format("Testing %s for all combinations of low/high qual... PASSED", read.getCigarString()));
         }
 
-
-
-
-
-        // ONE OFF Testing clipping that ends inside an insertion
+        // ONE OFF Testing clipping that ends inside an insertion  ( Ryan's bug )
         final byte[] BASES = {'A','C','G','T','A','C','G','T'};
         final byte[] QUALS = {2, 2, 2, 2, 20, 20, 20, 2};
         final String CIGAR = "1S1M5I1S";
@@ -179,14 +182,6 @@ public class ReadClipperUnitTest extends BaseTest {
         ClipReadsTestUtils.assertEqualReads(lowQualClipper.hardClipLowQualEnds((byte) 2), expected);
     }
 
-    private void testNoLowQualBases(GATKSAMRecord read, byte low_qual) {
-        if (!read.isEmpty()) {
-            byte [] quals = read.getBaseQualities();
-            for (int i=0; i<quals.length; i++)
-                Assert.assertFalse(quals[i] <= low_qual, String.format("Found low qual (%d) base after hard clipping. Position: %d -- %s", low_qual, i, read.getCigarString()));
-        }
-    }
-
     @Test(enabled = true)
     public void testHardClipSoftClippedBases() {
 
@@ -239,4 +234,14 @@ public class ReadClipperUnitTest extends BaseTest {
 //            logger.warn(String.format("Cigar %s -> %s -- PASSED!", read.getCigarString(), clippedRead.getCigarString()));
         }
     }
+
+    private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {
+        if (!read.isEmpty()) {
+            byte [] quals = read.getBaseQualities();
+            for (int i=0; i<quals.length; i++)
+                Assert.assertFalse(quals[i] <= low_qual, String.format("Found low qual (%d) base after hard clipping. Position: %d -- %s", low_qual, i, read.getCigarString()));
+        }
+    }
+
+
 }
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