/** * Create a BAMFileWriter that is ready to receive SAMRecords. Uses default compression level. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param outputFile where to write the output. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) { return makeBAMWriter(header, presorted, outputFile, this.getCompressionLevel()); }
/** * Create a BAMFileWriter that is ready to receive SAMRecords. Uses default compression level. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param outputPath where to write the output. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final Path outputPath) { return makeBAMWriter(header, presorted, outputPath, this.getCompressionLevel()); }
/** * Create a BAMFileWriter that is ready to receive SAMRecords. Uses default compression level. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param outputPath where to write the output. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final Path outputPath) { return makeBAMWriter(header, presorted, outputPath, this.getCompressionLevel()); }
/** * Create a BAMFileWriter that is ready to receive SAMRecords. Uses default compression level. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param outputFile where to write the output. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final File outputFile) { return makeBAMWriter(header, presorted, outputFile, this.getCompressionLevel()); }
/** * Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords. * This method does not support the creation of an MD5 file * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param stream the stream to write records to. Note that this method does not buffer the stream, so the * caller must buffer if desired. Note that PrintStream is buffered. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final OutputStream stream) { return initWriter(header, presorted, new BAMFileWriter(stream, (File)null, this.getCompressionLevel(), this.deflaterFactory)); }
/** * Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords. * This method does not support the creation of an MD5 file * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder. * @param stream the stream to write records to. Note that this method does not buffer the stream, so the * caller must buffer if desired. Note that PrintStream is buffered. */ public SAMFileWriter makeBAMWriter(final SAMFileHeader header, final boolean presorted, final OutputStream stream) { return initWriter(header, presorted, new BAMFileWriter(stream, (File)null, this.getCompressionLevel(), this.deflaterFactory)); }