public WorkaroundingStream(InputStream stream, SAMFileHeader header) { this.stream = stream; String text = header.getTextHeader(); if (text == null) { StringWriter writer = new StringWriter(); new SAMTextHeaderCodec().encode(writer, header); text = writer.toString(); } byte[] b; try { b = text.getBytes("UTF-8"); } catch (UnsupportedEncodingException e) { b = null; assert false; } headerRemaining = true; headerLength = b.length; headerStream = new ByteArrayInputStream(b); this.length = Long.MAX_VALUE; }
public WorkaroundingStream(InputStream stream, SAMFileHeader header) { this.stream = stream; String text = header.getTextHeader(); if (text == null) { StringWriter writer = new StringWriter(); new SAMTextHeaderCodec().encode(writer, header); text = writer.toString(); } byte[] b; try { b = text.getBytes("UTF-8"); } catch (UnsupportedEncodingException e) { b = null; assert false; } headerRemaining = true; headerLength = b.length; headerStream = new ByteArrayInputStream(b); this.length = Long.MAX_VALUE; }
public WorkaroundingStream(InputStream stream, SAMFileHeader header) { this.stream = stream; String text = header.getTextHeader(); if (text == null) { StringWriter writer = new StringWriter(); new SAMTextHeaderCodec().encode(writer, header); text = writer.toString(); } byte[] b; try { b = text.getBytes("UTF-8"); } catch (UnsupportedEncodingException e) { b = null; assert false; } headerRemaining = true; headerLength = b.length; headerStream = new ByteArrayInputStream(b); this.length = Long.MAX_VALUE; }
public String header() throws IOException { init(); return samReader.getFileHeader().getTextHeader(); }
FileSystem fs = FileSystem.get(conf); BufferedWriter br = new BufferedWriter(new OutputStreamWriter(fs.create(headerPath, true))); br.write(header.getTextHeader()); br.close();
System.out.println(cramHeader.getSamFileHeader().getTextHeader()); return;
System.out.println(cramHeader.getSamFileHeader().getTextHeader()); return;
final SAMFileHeader header = samReader.getFileHeader(); if (!RECORDS_ONLY) { if (header.getTextHeader() != null) { writer.write(header.getTextHeader()); } else {
final SAMFileHeader header = samReader.getFileHeader(); if (!RECORDS_ONLY) { if (header.getTextHeader() != null) { writer.write(header.getTextHeader()); } else {