From e93b025b393af24dabbaf336ed405482635645a6 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Fri, 6 Jul 2012 12:07:57 -0400
Subject: [PATCH] Fixing unit test

with the new clipping behavior for weird cigars, we no longer can assert the final number of bases in the unit test, so I'm taking this bit off the unit test.
---
 .../sting/utils/clipping/ReadClipperUnitTest.java      | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
index a819e41c7..22989b328 100644
--- a/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java
@@ -119,7 +119,6 @@ public class ReadClipperUnitTest extends BaseTest {
                     GATKSAMRecord clipLeft = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, i);
 
                     if (!clipLeft.isEmpty()) {
-//                        System.out.println(String.format("Left Tail [%d]: %s (%d,%d,%d : %d,%d,%d) -> %s (%d,%d,%d : %d,%d,%d)", i, cigar.toString(), read.getUnclippedStart(), read.getSoftStart(), read.getAlignmentStart(), read.getAlignmentEnd(), read.getSoftEnd(), read.getUnclippedEnd(), clipLeft.getCigarString(), clipLeft.getUnclippedStart(), clipLeft.getSoftStart(), clipLeft.getAlignmentStart(), clipLeft.getAlignmentEnd(), clipLeft.getSoftEnd(), clipLeft.getUnclippedEnd()));
                         Assert.assertTrue(clipLeft.getAlignmentStart() >= i + 1, String.format("Clipped alignment start (%d) is less the expected (%d): %s -> %s", clipLeft.getAlignmentStart(), i + 1, read.getCigarString(), clipLeft.getCigarString()));
                         assertUnclippedLimits(read, clipLeft);
                     }
@@ -137,7 +136,7 @@ public class ReadClipperUnitTest extends BaseTest {
             if (read.getSoftEnd() == alnEnd) {                                                                          // we can't test right clipping if the read has hanging soft clips on the right side
                 for (int i = alnStart; i <= alnEnd; i++) {
                     GATKSAMRecord clipRight = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, i);
-                    if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {  // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
+                    if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {         // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
                         Assert.assertTrue(clipRight.getAlignmentEnd() <= i - 1, String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
                         assertUnclippedLimits(read, clipRight);
                     }
@@ -278,7 +277,6 @@ public class ReadClipperUnitTest extends BaseTest {
     private void checkClippedReadsForLowQualEnds(GATKSAMRecord read, GATKSAMRecord clippedRead, byte lowQual, int nLowQualBases) {
         assertUnclippedLimits(read, clippedRead);                                                                       // Make sure limits haven't changed
         assertNoLowQualBases(clippedRead, lowQual);                                                                     // Make sure the low qualities are gone
-        assertNumberOfBases(read, clippedRead, nLowQualBases);                                                          // Make sure only low quality bases were clipped
     }
 
     /**
@@ -294,12 +292,6 @@ public class ReadClipperUnitTest extends BaseTest {
         }
     }
 
-    private void assertNumberOfBases(GATKSAMRecord read, GATKSAMRecord clipLeft, int nLowQualBases) {
-        if (read.getCigarString().contains("M"))
-            Assert.assertEquals(clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, String.format("Clipped read size (%d) is different than the number high qual bases (%d) -- Cigars: %s -> %s", clipLeft.getReadLength(), read.getReadLength() - nLowQualBases, read.getCigarString(), clipLeft.getCigarString()));
-    }
-
-
     private boolean startsWithInsertion(Cigar cigar) {
         return leadingCigarElementLength(cigar, CigarOperator.INSERTION) > 0;
     }