@Override protected void writeHeader(final SAMFileHeader header) { new SAMTextHeaderCodec().encode(out, header); }
@Override protected SAMFileHeader readHeader(InputStream is) { SAMFileHeader samFileHeader = new SAMTextHeaderCodec().decode(new BufferedLineReader(is), null); return samFileHeader; } },
private void readHeader() { final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); mFileHeader = headerCodec.decode(mReader, (mFile != null ? mFile.toString() : null)); advanceLine(); }
public SAMSequenceDictionaryCodec(final BufferedWriter writer) { codec = new SAMTextHeaderCodec(); codec.setmFileHeader(EMPTY_HEADER); codec.setWriter(writer); }
@Override public String getSAMString() { return new SAMTextHeaderCodec().getPGLine(this); } }
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"); } }
readGroups = new ArrayList<>(); while (advanceLine() != null) { final ParsedHeaderLine parsedHeaderLine = new ParsedHeaderLine(mCurrentLine); if (!parsedHeaderLine.isLineValid()) { parseHDLine(parsedHeaderLine); break; case PG: parsePGLine(parsedHeaderLine); break; case RG: parseRGLine(parsedHeaderLine); break; case SQ: parseSQLine(parsedHeaderLine); break; case CO:
@Override public String getSAMString() { return new SAMTextHeaderCodec().getRGLine(this); } }
@Override public String getSAMString() { return new SAMTextHeaderCodec().getSQLine(this); } }
/** * 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); }
/** * Reads text SAM header and converts to a SAMSequenceDictionary object. * @param reader Where to get header text from. * @param source Name of the input file, for error messages. May be null. * @return complete SAMSequenceDictionary object. */ public SAMSequenceDictionary decode(final LineReader reader, final String source) { return codec.decode(reader, source).getSequenceDictionary(); }
private void writePGLine(final SAMProgramRecord programRecord) { if (programRecord == null) { return; } final String[] fields = new String[2 + programRecord.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.PG; fields[1] = SAMProgramRecord.PROGRAM_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + programRecord.getProgramGroupId(); encodeTags(programRecord, fields, 2); println(StringUtil.join(FIELD_SEPARATOR, fields)); }
public void setValidationStringency(final ValidationStringency validationStringency) { codec.setValidationStringency(validationStringency); } }
protected String getRGLine(final SAMReadGroupRecord readGroup) { final String[] fields = new String[2 + readGroup.getAttributes().size()]; fields[0] = HEADER_LINE_START + HeaderRecordType.RG; fields[1] = SAMReadGroupRecord.READ_GROUP_ID_TAG + TAG_KEY_VALUE_SEPARATOR + readGroup.getReadGroupId(); encodeTags(readGroup, fields, 2); return StringUtil.join(FIELD_SEPARATOR, fields); }
public SAMSequenceDictionaryCodec(final BufferedWriter writer) { codec = new SAMTextHeaderCodec(); codec.setmFileHeader(EMPTY_HEADER); codec.setWriter(writer); }
readGroups = new ArrayList<SAMReadGroupRecord>(); while (advanceLine() != null) { final ParsedHeaderLine parsedHeaderLine = new ParsedHeaderLine(mCurrentLine); if (!parsedHeaderLine.isLineValid()) { parseHDLine(parsedHeaderLine); break; case PG: parsePGLine(parsedHeaderLine); break; case RG: parseRGLine(parsedHeaderLine); break; case SQ: parseSQLine(parsedHeaderLine); break; case CO:
@Override public String getSAMString() { return new SAMTextHeaderCodec().getPGLine(this); } }
@Override public String getSAMString() { return new SAMTextHeaderCodec().getRGLine(this); } }
@Override public String getSAMString() { return new SAMTextHeaderCodec().getSQLine(this); } }
/** * 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); }