X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamWriter_p.cpp;h=1b1a3f2136a4452e9a8509896b3c36c38b7873d7;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=a8fe370b5a374a192b1264894e932218bda58d28;hpb=2e049ed7f28881bce09653e60f5aea54bfd7afbf;p=bamtools.git

diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp
index a8fe370..1b1a3f2 100644
--- a/src/api/internal/BamWriter_p.cpp
+++ b/src/api/internal/BamWriter_p.cpp
@@ -2,15 +2,16 @@
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 6 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/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;
 
@@ -28,7 +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);
@@ -148,7 +149,7 @@ std::string BamWriterPrivate::GetErrorString(void) const {
 
 // returns whether BAM file is open for writing or not
 bool BamWriterPrivate::IsOpen(void) const {
-    return m_stream.IsOpen;
+    return m_stream.IsOpen();
 }
 
 // opens the alignment archive
@@ -158,8 +159,8 @@ bool BamWriterPrivate::Open(const string& filename,
 {
     try {
 
-        // open the BGZF file for writing, return failure if error
-        m_stream.Open(filename, "wb");
+        // open the BGZF file for writing
+        m_stream.Open(filename, IBamIODevice::WriteOnly);
 
         // write BAM file 'metadata' components
         WriteMagicNumber();
@@ -212,10 +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;