Field Detail

• VCF_CHARSET

  public static final Charset VCF_CHARSET

  The encoding used for VCF files: ISO-8859-1. When writing VCF4.3 is implemented, this should change to UTF-8.

Constructor Detail

• VCFEncoder

  public VCFEncoder​(VCFHeader header,
                    boolean allowMissingFieldsInHeader,
                    boolean outputTrailingFormatFields)

  Prepare a VCFEncoder that will encode records appropriate to the given VCF header, optionally allowing missing fields in the header.

Method Detail

• setVCFHeader

  @Deprecated
  public void setVCFHeader​(VCFHeader header)

  Deprecated.

  since 10/24/13 use the constructor

• setAllowMissingFieldsInHeader

  @Deprecated
  public void setAllowMissingFieldsInHeader​(boolean allow)

  Deprecated.

  since 10/24/13 use the constructor

• encode

  public String encode​(VariantContext context)

  encodes a VariantContext as a VCF line Depending on the use case it may be more efficient to write(Appendable, VariantContext) directly instead of creating an intermediate string.

  Returns:

  the VCF line

• write

  public void write​(Appendable vcfOutput,
                    VariantContext context)
             throws IOException

  encodes a VariantContext context as VCF, and writes it directly to an Appendable This may be more efficient than calling encode(VariantContext) and then writing the result since it avoids creating an intermediate string.

  Parameters:

  vcfOutput - the Appendable to write to

  context - the variant

  Throws:

  IOException

• formatVCFDouble

  public static String formatVCFDouble​(double d)

  Takes a double value and pretty prints it to a String for display

  Large doubles => gets %.2f style formatting Doubles < 1 / 10 but > 1/100 => get %.3f style formatting Double < 1/100 => %.3e formatting

  Parameters:

  d -

  Returns:

• addGenotypeData

  public void addGenotypeData​(VariantContext vc,
                              Map<Allele,​String> alleleMap,
                              List<String> genotypeFormatKeys,
                              StringBuilder builder)

• buildAlleleStrings

  public Map<Allele,​String> buildAlleleStrings​(VariantContext vc)