Fix fundamental bug in iterator parse offset with respect to reversal…

…s. Crack is bad.
ComparativeGenomicsToolkit · Oct 2, 2012 · 9b19965 · 9b19965
1 parent b5f115c
commit 9b19965
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Showing 5 changed files with 23 additions and 26 deletions.
diff --git a/api/hdf5_impl/hdf5BottomSegmentIterator.cpp b/api/hdf5_impl/hdf5BottomSegmentIterator.cpp
@@ -131,6 +131,7 @@ void HDF5BottomSegmentIterator::toReverse() const
 {
   assert (inRange() == true);
   _reversed = !_reversed;
+  swap(_startOffset, _endOffset);
 }
 
 void HDF5BottomSegmentIterator::toSite(hal_index_t position, bool slice) const
@@ -189,6 +190,10 @@ void HDF5BottomSegmentIterator::toSite(hal_index_t position, bool slice) const
      _startOffset = position - _bottomSegment.getStartPosition();
      _endOffset = _bottomSegment.getStartPosition() + _bottomSegment.getLength()
         - position - 1;
+     if (_reversed)
+     {
+       swap(_startOffset, _endOffset);
+     }
   }  
 }
 

diff --git a/api/hdf5_impl/hdf5TopSegmentIterator.cpp b/api/hdf5_impl/hdf5TopSegmentIterator.cpp
@@ -131,6 +131,7 @@ void HDF5TopSegmentIterator::toReverse() const
 {
   assert (inRange() == true);
   _reversed = !_reversed;
+  swap(_startOffset, _endOffset);
 }
 
 void HDF5TopSegmentIterator::toSite(hal_index_t position, bool slice) const
@@ -189,6 +190,10 @@ void HDF5TopSegmentIterator::toSite(hal_index_t position, bool slice) const
      _startOffset = position - _topSegment.getStartPosition();
      _endOffset = _topSegment.getStartPosition() + _topSegment.getLength()
         - position - 1;
+     if (_reversed)
+     {
+       swap(_startOffset, _endOffset);
+     }
   }  
 }
 

diff --git a/api/tests/halBottomSegmentTest.cpp b/api/tests/halBottomSegmentTest.cpp
@@ -477,14 +477,14 @@ void BottomSegmentIteratorReverseTest::checkCallBack(AlignmentConstPtr alignment
 
   CuAssertTrue(_testCase, ti->getStartPosition() == 1);
   CuAssertTrue(_testCase, ti->getLength() == 6);
-  CuAssertTrue(_testCase, bi2->getStartPosition() == 8);
+  CuAssertTrue(_testCase, bi2->getStartPosition() == 6);
   CuAssertTrue(_testCase, bi2->getLength() == 6);
 
   string buffer;
   ti->getString(buffer);
   CuAssertTrue(_testCase, buffer == "CCTACG");
   bi2->getString(buffer);
-  CuAssertTrue(_testCase, buffer == "CACGTA");
+  CuAssertTrue(_testCase, buffer == "CGTAGG");
 
   ti = parent1->getTopSegmentIterator();
   CuAssertTrue(_testCase, ti->getReversed() == false);

diff --git a/api/tests/halColumnIteratorTest.cpp b/api/tests/halColumnIteratorTest.cpp
@@ -459,44 +459,31 @@ void ColumnIteratorInvTest::checkGenome(const Genome* genome)
         if (colNumber >= 0 && colNumber < 10)
         {
           CuAssertTrue(_testCase, dnaIt->getReversed() == false);
-          CuAssertTrue(_testCase, 
-                       dnaIt->getArrayIndex() == (hal_index_t)colNumber);
 
           // inversion on bottom branch
           CuAssertTrue(_testCase, dadIt->getReversed() == true);
-          CuAssertTrue(_testCase, 
-                       dadIt->getArrayIndex() == 9 - (hal_index_t)colNumber);
 
           CuAssertTrue(_testCase, graIt->getReversed() == true);
-          CuAssertTrue(_testCase, 
-                       graIt->getArrayIndex() == 9 - (hal_index_t)colNumber);
         }
         else if (colNumber >= 10 && colNumber < 20)
         {
           CuAssertTrue(_testCase, dnaIt->getReversed() == false);
-          CuAssertTrue(_testCase, 
-                       dnaIt->getArrayIndex() == (hal_index_t)colNumber);
 
           // inversion on bottom branch
           CuAssertTrue(_testCase, dadIt->getReversed() == true);
-          CuAssertTrue(_testCase, 
-                       dadIt->getArrayIndex() == 29 - (hal_index_t)colNumber);
 
           // inversion on top branch
           CuAssertTrue(_testCase, graIt->getReversed() == false);
-          CuAssertTrue(_testCase, 
-                       graIt->getArrayIndex() == (hal_index_t)colNumber);
 
         }
-        else
-        {
-          CuAssertTrue(_testCase, 
-                       dnaIt->getArrayIndex() == (hal_index_t)colNumber);
-          CuAssertTrue(_testCase, 
-                       dadIt->getArrayIndex() == (hal_index_t)colNumber);
-          CuAssertTrue(_testCase, 
-                       graIt->getArrayIndex() == (hal_index_t)colNumber);
-        }
+
+        CuAssertTrue(_testCase, 
+                     dnaIt->getArrayIndex() == (hal_index_t)colNumber);
+        CuAssertTrue(_testCase, 
+                     dadIt->getArrayIndex() == (hal_index_t)colNumber);
+        CuAssertTrue(_testCase, 
+                     graIt->getArrayIndex() == (hal_index_t)colNumber);
+
       }
     }
   }
@@ -947,7 +934,7 @@ void ColumnIteratorMultiGapInvTest::checkCallBack(AlignmentConstPtr alignment)
       CuAssertTrue(_testCase, entry->size() == 1);
       DNAIteratorConstPtr dna = entry->at(0);
       CuAssertTrue(_testCase, dna->getSequence() == adamSeq);
-      CuAssertTrue(_testCase, dna->getArrayIndex() == 11 - i);
+      CuAssertTrue(_testCase, dna->getArrayIndex() == i);
 
       CuAssertTrue(_testCase, colMap->find(grandpaSeq) != colMap->end());
       entry = colMap->find(grandpaSeq)->second;

diff --git a/api/tests/halTopSegmentTest.cpp b/api/tests/halTopSegmentTest.cpp
@@ -462,14 +462,14 @@ void TopSegmentIteratorReverseTest::checkCallBack(AlignmentConstPtr alignment)
 
   CuAssertTrue(_testCase, bi->getStartPosition() == 1);
   CuAssertTrue(_testCase, bi->getLength() == 6);
-  CuAssertTrue(_testCase, ti2->getStartPosition() == 8);
+  CuAssertTrue(_testCase, ti2->getStartPosition() == 6);
   CuAssertTrue(_testCase, ti2->getLength() == 6);
 
   string buffer;
   bi->getString(buffer);
   CuAssertTrue(_testCase, buffer == "CCTACG");
   ti2->getString(buffer);
-  CuAssertTrue(_testCase, buffer == "CACGTA");
+  CuAssertTrue(_testCase, buffer == "CGTAGG");
 
   bi = child1->getBottomSegmentIterator();
   CuAssertTrue(_testCase, bi->getReversed() == false);