X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamWriter_p.cpp;h=1b1a3f2136a4452e9a8509896b3c36c38b7873d7;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=100de2d2d25a378c64179e39e71e6fdf874eb847;hpb=2e1822c9ed231b25fd474117a01a1492d4209fa4;p=bamtools.git

diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp
index 100de2d..1b1a3f2 100644
--- a/src/api/internal/BamWriter_p.cpp
+++ b/src/api/internal/BamWriter_p.cpp
@@ -2,16 +2,16 @@
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************
 
-#include <api/BamAlignment.h>
-#include <api/BamConstants.h>
-#include <api/IBamIODevice.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamWriter_p.h>
+#include "api/BamAlignment.h"
+#include "api/BamConstants.h"
+#include "api/IBamIODevice.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamWriter_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -29,7 +29,7 @@ BamWriterPrivate::~BamWriterPrivate(void) {
     Close();
 }
 
-// calculates minimum bin for a BAM alignment interval
+// calculates minimum bin for a BAM alignment interval [begin, end)
 uint32_t BamWriterPrivate::CalculateMinimumBin(const int begin, int end) const {
     --end;
     if ( (begin >> 14) == (end >> 14) ) return 4681 + (begin >> 14);
@@ -160,7 +160,7 @@ bool BamWriterPrivate::Open(const string& filename,
     try {
 
         // open the BGZF file for writing
-        m_stream.Open(filename,  IBamIODevice::WriteOnly);
+        m_stream.Open(filename, IBamIODevice::WriteOnly);
 
         // write BAM file 'metadata' components
         WriteMagicNumber();
@@ -213,10 +213,9 @@ void BamWriterPrivate::WriteAlignment(const BamAlignment& al) {
     const unsigned int queryLength        = al.QueryBases.size();
     const unsigned int tagDataLength      = al.TagData.size();
 
-    // no way to tell if BamAlignment.Bin is already defined (no default, invalid value)
-    // force calculation of Bin before storing
-    const int endPosition = al.GetEndPosition();
-    const uint32_t alignmentBin = CalculateMinimumBin(al.Position, endPosition);
+    // no way to tell if alignment's bin is already defined (there is no default, invalid value)
+    // so we'll go ahead calculate its bin ID before storing
+    const uint32_t alignmentBin = CalculateMinimumBin(al.Position, al.GetEndPosition());
 
     // create our packed cigar string
     string packedCigar;