X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamRandomAccessController_p.cpp;h=1e44b7daef47ccc52e96df28c6e1471b7e9cf270;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=7f5c3506a9fc85d4912c0fec99c8fae620f0c759;hpb=2e049ed7f28881bce09653e60f5aea54bfd7afbf;p=bamtools.git

diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp
index 7f5c350..1e44b7d 100644
--- a/src/api/internal/BamRandomAccessController_p.cpp
+++ b/src/api/internal/BamRandomAccessController_p.cpp
@@ -2,16 +2,16 @@
 // BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 6 October 2011(DB)
+// Last modified: 10 October 2011(DB)
 // ---------------------------------------------------------------------------
 // Manages random access operations in a BAM file
 // **************************************************************************
 
-#include <api/BamIndex.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamIndexFactory_p.h>
+#include "api/BamIndex.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamIndexFactory_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -79,9 +79,9 @@ BamRandomAccessController::AlignmentState(const BamAlignment& alignment) const {
         // if alignment starts at or after left bound position
         if ( alignment.Position >= m_region.LeftPosition) {
 
-            if ( m_region.isRightBoundSpecified() &&            // right bound is specified AND
-                 m_region.LeftRefID == m_region.RightRefID &&   // left & right bounds on same reference AND
-                 alignment.Position > m_region.RightPosition )  // alignment starts after right bound position
+            if ( m_region.isRightBoundSpecified() &&             // right bound is specified AND
+                 m_region.LeftRefID == m_region.RightRefID &&    // left & right bounds on same reference AND
+                 alignment.Position >= m_region.RightPosition )  // alignment starts on or after right bound position
                 return AfterRegion;
 
             // otherwise, alignment overlaps region
@@ -92,7 +92,7 @@ BamRandomAccessController::AlignmentState(const BamAlignment& alignment) const {
         else {
 
             // if alignment overlaps left bound position
-            if ( alignment.GetEndPosition() >= m_region.LeftPosition )
+            if ( alignment.GetEndPosition() > m_region.LeftPosition )
                 return OverlapsRegion;
             else
                 return BeforeRegion;
@@ -116,15 +116,15 @@ BamRandomAccessController::AlignmentState(const BamAlignment& alignment) const {
             // alignment is on right bound reference
             else {
 
-                // if alignment starts on or before right bound position
-                if ( alignment.Position <= m_region.RightPosition )
+                // if alignment starts before right bound position
+                if ( alignment.Position < m_region.RightPosition )
                     return OverlapsRegion;
                 else
                     return AfterRegion;
             }
         }
 
-        // otherwise, alignment starts after left bound and there is no right bound
+        // otherwise, alignment starts after left bound and there is no right bound given
         else return OverlapsRegion;
     }
 }