Extension of BamReader BamWriter API

src/api/BamReader.cpp

@@ -276,6 +276,22 @@ bool BamReader::Open(const std::string& filename) {
     return d->Open(filename);
 }
 
+/*! \fn bool BamReader::Open(const std::string& filename, IBamIODevice* device)
+    \brief Opens a BAM file with a custom io device.
+
+    If BamReader is already opened on another file, this function closes
+    that file, then attempts to open requested \a filename.
+
+    \param[in] filename name of BAM file to open
+
+    \returns \c true if BAM file was opened successfully
+    \sa Close(), IsOpen(), OpenIndex()
+*/
+bool BamReader::Open(const std::string& filename, IBamIODevice* device)
+{
+	return d->Open(filename, device);
+}
+
 /*! \fn bool BamReader::OpenIndex(const std::string& indexFilename)
     \brief Opens a BAM index file.
 

src/api/BamReader.h

@@ -1,4 +1,4 @@
-// ***************************************************************************
+// ***************************************************************************
 // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
@@ -14,6 +14,7 @@
 #include "api/BamAlignment.h"
 #include "api/BamIndex.h"
 #include "api/SamHeader.h"
+#include "api/IBamIODevice.h"
 #include <string>
 
 namespace BamTools {
@@ -46,6 +47,8 @@ class API_EXPORT BamReader {
         bool Jump(int refID, int position = 0);
         // opens a BAM file
         bool Open(const std::string& filename);
+        // opens a BAM file with a custom io device. Device is deleted by BamReader so it must be created on a heap 
+        bool Open(const std::string& filename, IBamIODevice* device);
         // returns internal file pointer to beginning of alignment data
         bool Rewind(void);
         // sets the target region of interest

src/api/BamWriter.cpp

@@ -96,6 +96,15 @@ bool BamWriter::Open(const std::string& filename,
     return d->Open(filename, samHeaderText, referenceSequences);
 }
 
+bool BamWriter::Open(const std::string& filename,
+            const SamHeader& samHeader,
+            const RefVector& referenceSequences,
+			IBamIODevice* device)
+{
+	return d->Open(filename, samHeader.ToString(), referenceSequences, device);
+}
+
+
 /*! \fn bool BamWriter::Open(const std::string& filename,
                              const SamHeader& samHeader,
                              const RefVector& referenceSequences)

src/api/BamWriter.h

@@ -12,6 +12,7 @@
 
 #include "api/api_global.h"
 #include "api/BamAux.h"
+#include "api/IBamIODevice.h"
 #include <string>
 
 namespace BamTools {
@@ -54,6 +55,12 @@ class API_EXPORT BamWriter {
         bool Open(const std::string& filename,
                   const SamHeader& samHeader,
                   const RefVector& referenceSequences);
+		// opens a BAM file for writing using a custom oi device
+		// Device is deleted by BamWriter so it must be created on a heap 
+        bool Open(const std::string& filename,
+                  const SamHeader& samHeader,
+                  const RefVector& referenceSequences,
+				  IBamIODevice* device);		
         // saves the alignment to the alignment archive
         bool SaveAlignment(const BamAlignment& alignment);
         // sets the output compression mode

src/api/internal/bam/BamReader_p.cpp

@@ -363,15 +363,15 @@ bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) {
 }
 
 // opens BAM file (and index)
-bool BamReaderPrivate::Open(const string& filename) {
+bool BamReaderPrivate::Open(const string& filename, IBamIODevice* device) {
 
     try {
 
         // make sure we're starting with fresh state
         Close();
 
         // open BgzfStream
-        m_stream.Open(filename, IBamIODevice::ReadOnly);
+        m_stream.Open(filename, IBamIODevice::ReadOnly, device);
 
         // load BAM metadata
         LoadHeaderData();

src/api/internal/bam/BamReader_p.h

@@ -27,6 +27,7 @@
 #include "api/internal/bam/BamHeader_p.h"
 #include "api/internal/bam/BamRandomAccessController_p.h"
 #include "api/internal/io/BgzfStream_p.h"
+#include "api/IBamIODevice.h"
 #include <string>
 
 namespace BamTools {
@@ -46,7 +47,7 @@ class BamReaderPrivate {
         bool Close(void);
         const std::string Filename(void) const;
         bool IsOpen(void) const;
-        bool Open(const std::string& filename);
+        bool Open(const std::string& filename, IBamIODevice* device = 0);
         bool Rewind(void);
         bool SetRegion(const BamRegion& region);
 

src/api/internal/bam/BamWriter_p.cpp

@@ -155,12 +155,13 @@ bool BamWriterPrivate::IsOpen(void) const {
 // opens the alignment archive
 bool BamWriterPrivate::Open(const string& filename,
                             const string& samHeaderText,
-                            const RefVector& referenceSequences)
+                            const RefVector& referenceSequences,
+							IBamIODevice* device)
 {
     try {
 
         // open the BGZF file for writing
-        m_stream.Open(filename, IBamIODevice::WriteOnly);
+        m_stream.Open(filename, IBamIODevice::WriteOnly, device);
 
         // write BAM file 'metadata' components
         WriteMagicNumber();

src/api/internal/bam/BamWriter_p.h

@@ -22,6 +22,7 @@
 
 #include "api/BamAux.h"
 #include "api/internal/io/BgzfStream_p.h"
+#include "api/IBamIODevice.h"
 #include <string>
 #include <vector>
 
@@ -45,7 +46,8 @@ class BamWriterPrivate {
         bool IsOpen(void) const;
         bool Open(const std::string& filename,
                   const std::string& samHeaderText,
-                  const BamTools::RefVector& referenceSequences);
+                  const BamTools::RefVector& referenceSequences,
+				  IBamIODevice* device = 0);
         bool SaveAlignment(const BamAlignment& al);
         void SetWriteCompressed(bool ok);
 

src/api/internal/io/BgzfStream_p.cpp

@@ -268,15 +268,21 @@ bool BgzfStream::IsOpen(void) const {
     return m_device->IsOpen();
 }
 
-void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode) {
+void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode, IBamIODevice* device) {
 
     // close current device if necessary
     Close();
     BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
 
     // retrieve new IO device depending on filename
-    m_device = BamDeviceFactory::CreateDevice(filename);
-    BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from filename" );
+	// or use the device provided by the client
+    if (device == 0) {
+        m_device = BamDeviceFactory::CreateDevice(filename);
+    }
+    else {
+        m_device = device;
+    }
+	BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from filename" );
 
     // if device fails to open
     if ( !m_device->Open(mode) ) {

src/api/internal/io/BgzfStream_p.h

@@ -44,7 +44,7 @@ class BgzfStream {
         // returns true if BgzfStream open for IO
         bool IsOpen(void) const;
         // opens the BGZF file
-        void Open(const std::string& filename, const IBamIODevice::OpenMode mode);
+        void Open(const std::string& filename, const IBamIODevice::OpenMode mode, IBamIODevice* device = 0);
         // reads BGZF data into a byte buffer
         size_t Read(char* data, const size_t dataLength);
         // seek to position in BGZF file