+/*! \fn bool BamWriter::Open(const std::string& filename,\r
+ const SamHeader& samHeader,\r
+ const RefVector& referenceSequences)\r
+ \brief Opens a BAM file for writing.\r
+\r
+ This is an overloaded function.\r
+\r
+ Will overwrite the BAM file if it already exists.\r
+\r
+ \param[in] filename name of output BAM file\r
+ \param[in] samHeader header data, wrapped in SamHeader object\r
+ \param[in] referenceSequences list of reference entries\r
+\r
+ \return \c true if opened successfully\r
+ \sa Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData()\r
+*/\r
+bool BamWriter::Open(const std::string& filename,\r
+ const SamHeader& samHeader,\r
+ const RefVector& referenceSequences)\r
+{\r
+ return d->Open(filename, samHeader.ToString(), referenceSequences);\r
+}\r
+\r
+/*! \fn void BamWriter::SaveAlignment(const BamAlignment& alignment)\r
+ \brief Saves an alignment to the BAM file.\r
+\r
+ \param[in] alignment BamAlignment record to save\r
+ \sa BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore()\r
+*/\r
+bool BamWriter::SaveAlignment(const BamAlignment& alignment) {\r
+ return d->SaveAlignment(alignment);\r
+}\r
+\r
+/*! \fn void BamWriter::SetCompressionMode(const BamWriter::CompressionMode& compressionMode)\r
+ \brief Sets the output compression mode.\r
+\r
+ Default mode is BamWriter::Compressed.\r
+\r
+ \note Changing the compression mode is disabled on open files (i.e. the request will\r
+ be ignored). Be sure to call this function before opening the BAM file.\r
+\r
+ \code\r
+ BamWriter writer;\r
+ writer.SetCompressionMode(BamWriter::Uncompressed);\r
+ writer.Open( ... );\r
+ // ...\r
+ \endcode\r
+\r
+ \param[in] compressionMode desired output compression behavior\r
+ \sa IsOpen(), Open()\r
+*/\r
+void BamWriter::SetCompressionMode(const BamWriter::CompressionMode& compressionMode) {\r
+ d->SetWriteCompressed( compressionMode == BamWriter::Compressed );\r