Package htsjdk.samtools

Class SAMTextHeaderCodec

  • public class SAMTextHeaderCodec
extends Object
    Parser for a SAM text header, and a generator of SAM text header.

    • 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.

      • setValidationStringency

        public void setValidationStringency​(ValidationStringency validationStringency)