Package htsjdk.variant.vcf

Class VCFEncoder

java.lang.Object
htsjdk.variant.vcf.VCFEncoder
public class VCFEncoder extends Object
Functions specific to encoding VCF records.

  • Field Details

    • 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 Details

    • 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 Details

    • 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)