/** * Convert SAMFileHeader from in-memory representation to text representation. Always writes * SAMFileHeader.CURRENT_VERSION as the version in the header. * @param writer where to write the header text. * @param header object to be converted to text. */ public void encode(final Writer writer, final SAMFileHeader header) { encode(writer, header, false); }
/** * Convert SAMFileHeader from in-memory representation to text representation. Always writes * SAMFileHeader.CURRENT_VERSION as the version in the header. * @param writer where to write the header text. * @param header object to be converted to text. */ public void encode(final Writer writer, final SAMFileHeader header) { encode(writer, header, false); }
/** * Convert SAMFileHeader from in-memory representation to text representation. Always writes * SAMFileHeader.CURRENT_VERSION as the version in the header. * @param writer where to write the header text. * @param header object to be converted to text. */ public void encode(final Writer writer, final SAMFileHeader header) { encode(writer, header, false); }
@Override protected void writeHeader(final SAMFileHeader header) { new SAMTextHeaderCodec().encode(out, header); }
@Override public String getSAMString() { final StringWriter stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, this); return stringWriter.toString(); }
@Override public String getSAMString() { final StringWriter stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, this); return stringWriter.toString(); }
@Override protected void writeHeader(final SAMFileHeader header) { new SAMTextHeaderCodec().encode(out, header); }
/** * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the * samFileHeader and the String, use the version of this method which takes both. */ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) { // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made final String headerString; final Writer stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true); headerString = stringWriter.toString(); writeHeader(outputBinaryCodec, samFileHeader, headerString); }
/** * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the * samFileHeader and the String, use the version of this method which takes both. */ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) { // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made final String headerString; final Writer stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true); headerString = stringWriter.toString(); writeHeader(outputBinaryCodec, samFileHeader, headerString); }
public void writeHeader(final SAMFileHeader header) { final StringWriter headerTextBuffer = new StringWriter(); new SAMTextHeaderCodec().encode(headerTextBuffer, header); final String headerText = headerTextBuffer.toString(); super.writeHeader(headerText); } }
/** * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the * samFileHeader and the String, use the version of this method which takes both. */ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) { // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made final String headerString; final Writer stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true); headerString = stringWriter.toString(); writeHeader(outputBinaryCodec, samFileHeader, headerString); }
public void writeHeader(final SAMFileHeader header) { final StringWriter headerTextBuffer = new StringWriter(); new SAMTextHeaderCodec().encode(headerTextBuffer, header); final String headerText = headerTextBuffer.toString(); super.writeHeader(headerText); } }
/** * Writes a header to a BAM file. Might need to regenerate the String * version of the header, if one already has both the samFileHeader and the * String, use the version of this method which takes both. */ static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) { // Do not use SAMFileHeader.getTextHeader() as it is not updated when // changes to the underlying object are made final String headerString; final Writer stringWriter = new StringWriter(); new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true); headerString = stringWriter.toString(); writeHeader(outputBinaryCodec, samFileHeader, headerString); }
/** * Write the header to disk. Header object is available via getHeader(). * * <p>IMPORTANT: this method will be abstract once {@link #writeHeader(String)} is removed. * * <p>Note: default implementation uses {@link SAMTextHeaderCodec#encode} and calls * {@link #writeHeader(String)}. * * @param header object to write. */ protected void writeHeader(final SAMFileHeader header) { final StringWriter headerTextBuffer = new StringWriter(); new SAMTextHeaderCodec().encode(headerTextBuffer, header); writeHeader(headerTextBuffer.toString()); }
/** * Write the header to disk. Header object is available via getHeader(). * * <p>IMPORTANT: this method will be abstract once {@link #writeHeader(String)} is removed. * * <p>Note: default implementation uses {@link SAMTextHeaderCodec#encode} and calls * {@link #writeHeader(String)}. * * @param header object to write. */ protected void writeHeader(final SAMFileHeader header) { final StringWriter headerTextBuffer = new StringWriter(); new SAMTextHeaderCodec().encode(headerTextBuffer, header); writeHeader(headerTextBuffer.toString()); }
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 final SAMFileHeader clone() { final SAMTextHeaderCodec codec = new SAMTextHeaderCodec(); codec.setValidationStringency(ValidationStringency.SILENT); final StringWriter stringWriter = new StringWriter(); codec.encode(stringWriter, this); return codec.decode(new StringLineReader(stringWriter.toString()), "SAMFileHeader.clone"); } }
private void writeHeader(final SAMFileHeader header) { binaryCodec.writeBytes("BAM\001".getBytes(Charset.forName("UTF8"))); final Writer sw = new StringWriter(); new SAMTextHeaderCodec().encode(sw, header); binaryCodec.writeString(sw.toString(), true, false); final SAMSequenceDictionary dict = header.getSequenceDictionary(); binaryCodec.writeInt(dict.size()); for (final SAMSequenceRecord rec : dict.getSequences()) { binaryCodec.writeString(rec.getSequenceName(), true, true); binaryCodec.writeInt (rec.getSequenceLength()); } } }
private void writeHeader(final SAMFileHeader header) { binaryCodec.writeBytes("BAM\001".getBytes(Charset.forName("UTF8"))); final Writer sw = new StringWriter(); new SAMTextHeaderCodec().encode(sw, header); binaryCodec.writeString(sw.toString(), true, false); final SAMSequenceDictionary dict = header.getSequenceDictionary(); binaryCodec.writeInt(dict.size()); for (final SAMSequenceRecord rec : dict.getSequences()) { binaryCodec.writeString(rec.getSequenceName(), true, true); binaryCodec.writeInt (rec.getSequenceLength()); } } }
private void writeHeader(final SAMFileHeader header) { binaryCodec.writeBytes("BAM\001".getBytes(Charset.forName("UTF8"))); final Writer sw = new StringWriter(); new SAMTextHeaderCodec().encode(sw, header); binaryCodec.writeString(sw.toString(), true, false); final SAMSequenceDictionary dict = header.getSequenceDictionary(); binaryCodec.writeInt(dict.size()); for (final SAMSequenceRecord rec : dict.getSequences()) { binaryCodec.writeString(rec.getSequenceName(), true, true); binaryCodec.writeInt (rec.getSequenceLength()); } } }