Basic internal implementation of BamFile & BamPipe

[bamtools.git] / src / api / internal / BamFile_p.cpp

diff --git a/src/api/internal/BamFile_p.cpp b/src/api/internal/BamFile_p.cpp
new file mode 100644 (file)
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+++ b/src/api/internal/BamFile_p.cpp
@@ -0,0 +1,95 @@
+// ***************************************************************************
+// BamFile_p.cpp (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 8 September 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides reading of local BAM files
+// ***************************************************************************
+
+#include <api/internal/BamFile_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+using namespace std;
+
+BamFile::BamFile(const string& filename)
+    : IBamIODevice()
+    , m_stream(0)
+    , m_filename(filename)
+{ }
+
+BamFile::~BamFile(void) {
+    Close();
+}
+
+void BamFile::Close(void) {
+
+    // skip if not open
+    if ( !IsOpen() )
+        return;
+
+    // flush & close FILE*
+    fflush(m_stream);
+    fclose(m_stream);
+
+    // reset internals
+    m_mode = IBamIODevice::NotOpen;
+    m_stream = 0;
+    m_filename.clear();
+}
+
+bool BamFile::IsRandomAccess(void) const {
+    return true;
+}
+
+bool BamFile::Open(const IBamIODevice::OpenMode mode) {
+
+    // make sure we're starting with a fresh file stream
+    Close();
+
+    // attempt to open FILE* depending on requested openmode
+    if ( mode == IBamIODevice::ReadOnly )
+        m_stream = fopen(m_filename.c_str(), "rb");
+    else if ( mode == IBamIODevice::WriteOnly )
+        m_stream = fopen(m_filename.c_str(), "wb");
+    else {
+        SetErrorString("BamFile ERROR - unknown device open mode");
+        return false;
+    }
+
+    // check that we obtained a valid FILE*
+    if ( m_stream == 0 ) {
+        string error = "BamFile ERROR - could not open handle on ";
+        error += ( (m_filename.empty()) ? "empty filename" : m_filename );
+        SetErrorString(error);
+        return false;
+    }
+
+    // store current IO mode & return success
+    m_mode = mode;
+    return true;
+}
+
+size_t BamFile::Read(char* data, const unsigned int numBytes) {
+    BT_ASSERT_X( m_stream, "BamFile::Read() - null stream" );
+    BT_ASSERT_X( (m_mode == IBamIODevice::ReadOnly), "BamFile::Read() - device not in read-only mode");
+    return fread(data, sizeof(char), numBytes, m_stream);
+}
+
+bool BamFile::Seek(const int64_t& position) {
+    BT_ASSERT_X( m_stream, "BamFile::Seek() - null stream" );
+    return ( fseek64(m_stream, position, SEEK_SET) == 0);
+}
+
+int64_t BamFile::Tell(void) const {
+    BT_ASSERT_X( m_stream, "BamFile::Tell() - null stream" );
+    return ftell64(m_stream);
+}
+
+size_t BamFile::Write(const char* data, const unsigned int numBytes) {
+    BT_ASSERT_X( m_stream, "BamFile::Write() - null stream" );
+    BT_ASSERT_X( (m_mode == IBamIODevice::WriteOnly), "BamFile::Write() - device not in write-only mode" );
+    return fwrite(data, sizeof(char), numBytes, m_stream);
+}