/** * Create a CRAMFileWriter on an output file. * * Note: does not honor factory setting for USE_ASYNC_IO. * * @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 output where to write the output. Must end with .sam, .bam or .cram. * @param referenceFasta reference sequence file * @return CRAMFileWriter * */ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean presorted, final Path output, final Path referenceFasta) { return createCRAMWriterWithSettings(header, presorted, output, referenceFasta); }
/** * Create a CRAMFileWriter on an output file. * * Note: does not honor factory setting for USE_ASYNC_IO. * * @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 output where to write the output. Must end with .sam, .bam or .cram. * @param referenceFasta reference sequence file * @return CRAMFileWriter * */ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final boolean presorted, final Path output, final Path referenceFasta) { return createCRAMWriterWithSettings(header, presorted, output, referenceFasta); }
/** * Create a CRAMFileWriter on an output file. Requires input record to be presorted to match the * sort order defined by the input header. * * Note: does not honor factory settings for USE_ASYNC_IO. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param outputFile where to write the output. Must end with .sam, .bam or .cram. * @param referenceFasta reference sequence file * @return CRAMFileWriter * */ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final File outputFile, final File referenceFasta) { return createCRAMWriterWithSettings(header, true, outputFile.toPath(), IOUtil.toPath( referenceFasta )); }
/** * Create a CRAMFileWriter on an output file. Requires input record to be presorted to match the * sort order defined by the input header. * * Note: does not honor factory settings for USE_ASYNC_IO. * * @param header entire header. Sort order is determined by the sortOrder property of this arg. * @param outputFile where to write the output. Must end with .sam, .bam or .cram. * @param referenceFasta reference sequence file * @return CRAMFileWriter * */ public CRAMFileWriter makeCRAMWriter(final SAMFileHeader header, final File outputFile, final File referenceFasta) { return createCRAMWriterWithSettings(header, true, outputFile.toPath(), IOUtil.toPath( referenceFasta )); }