Package htsjdk.samtools

Class SAMTextHeaderCodec

java.lang.Object
htsjdk.samtools.SAMTextHeaderCodec
public class SAMTextHeaderCodec extends Object
Parser for a SAM text header, and a generator of SAM text header.

  • Field Details

    • COMMENT_PREFIX

      public static final String COMMENT_PREFIX

  • Constructor Details

    • SAMTextHeaderCodec

      public SAMTextHeaderCodec()

  • Method Details

    • 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)