Field Detail

• COMMENT_PREFIX

  public static final String COMMENT_PREFIX

Constructor Detail

• SAMTextHeaderCodec

  public SAMTextHeaderCodec()

Method Detail

• decode

  public SAMFileHeader decode​(LineReader reader,
                              String source)

  Reads text SAM header and converts to a SAMFileHeader object.

  Parameters:

  reader - Where to get header text from.

  source - Name of the input file, for error messages. May be null.

  Returns:

  complete header object.

• encode

  public void encode​(Writer writer,
                     SAMFileHeader header)

  Convert SAMFileHeader from in-memory representation to text representation. Always writes SAMFileHeader.CURRENT_VERSION as the version in the header.

  Parameters:

  writer - where to write the header text.

  header - object to be converted to text.

• encode

  public void encode​(Writer writer,
                     SAMFileHeader header,
                     boolean keepExistingVersionNumber)

  Convert SAMFileHeader from in-memory representation to text representation.

  Parameters:

  writer - where to write the header text.

  header - object to be converted to text.

  keepExistingVersionNumber - If true, writes whatever version # was in the header. If false, writes SAMFileHeader.CURRENT_VERSION.

• getPGLine

  protected String getPGLine​(SAMProgramRecord programRecord)

• getRGLine

  protected String getRGLine​(SAMReadGroupRecord readGroup)

• getSQLine

  protected String getSQLine​(SAMSequenceRecord sequenceRecord)

• setValidationStringency

  public void setValidationStringency​(ValidationStringency validationStringency)