/** * Write a CRAM File header and a SAM Header to an output stream. * * @param cramVersion * @param outStream * @param samFileHeader * @param cramID * @return the offset in the stream after writing the headers */ public static long writeHeader(final Version cramVersion, final OutputStream outStream, final SAMFileHeader samFileHeader, String cramID) { final CramHeader cramHeader = new CramHeader(cramVersion, cramID, samFileHeader); return CramIO.writeCramHeader(cramHeader, outStream); }
/** * Write a CRAM File header and a SAM Header to an output stream. * * @param cramVersion * @param outStream * @param samFileHeader * @param cramID * @return the offset in the stream after writing the headers */ public static long writeHeader(final Version cramVersion, final OutputStream outStream, final SAMFileHeader samFileHeader, String cramID) { final CramHeader cramHeader = new CramHeader(cramVersion, cramID, samFileHeader); try { return CramIO.writeCramHeader(cramHeader, outStream); } catch (final IOException e) { throw new RuntimeIOException(e); } }
@Test public void testCheckHeaderAndEOF_v2() throws IOException { final String id = "testid"; final CramHeader cramHeader = new CramHeader(CramVersions.CRAM_v2_1, id, new SAMFileHeader()); final File file = File.createTempFile("test", ".cram"); file.deleteOnExit(); final FileOutputStream fos = new FileOutputStream(file); CramIO.writeCramHeader(cramHeader, fos); CramIO.issueEOF(cramHeader.getVersion(), fos); fos.close(); Assert.assertTrue(CramIO.checkHeaderAndEOF(file)); file.delete(); }
@Test public void testCheckHeaderAndEOF_v3() throws IOException { final String id = "testid"; final CramHeader cramHeader = new CramHeader(CramVersions.CRAM_v3, id, new SAMFileHeader()); final File file = File.createTempFile("test", ".cram"); file.deleteOnExit(); final FileOutputStream fos = new FileOutputStream(file); CramIO.writeCramHeader(cramHeader, fos); CramIO.issueEOF(cramHeader.getVersion(), fos); fos.close(); Assert.assertTrue(CramIO.checkHeaderAndEOF(file)); file.delete(); }
ValidationStringency.SILENT, null); CramHeader cramHeader = new CramHeader(CramVersions.CRAM_v3, new File(args[0]).getName(), samFileHeader); CramIO.writeCramHeader(cramHeader, cramOutputStream);
file.deleteOnExit(); final FileOutputStream fos = new FileOutputStream(file); CramIO.writeCramHeader(cramHeader, fos); CramIO.issueEOF(cramHeader.getVersion(), fos); fos.close();