Package htsjdk.variant.vcf

Class VCFCompoundHeaderLine

java.lang.Object
htsjdk.variant.vcf.VCFHeaderLine
htsjdk.variant.vcf.VCFCompoundHeaderLine
All Implemented Interfaces:
VCFIDHeaderLine, Serializable, Comparable
Direct Known Subclasses:
VCFFormatHeaderLine, VCFInfoHeaderLine
public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFIDHeaderLine
a base class for compound header lines, which include info lines and format lines (so far)
See Also:

  • Constructor Details

    • VCFCompoundHeaderLine

      protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
      create a VCF format header line
      Parameters:
      name - the name for this header line
      count - the count for this header line
      type - the type for this header line
      description - the description for this header line
      lineType - the header line type

    • VCFCompoundHeaderLine

      protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
      create a VCF format header line
      Parameters:
      name - the name for this header line
      count - the count type for this header line
      type - the type for this header line
      description - the description for this header line
      lineType - the header line type

    • VCFCompoundHeaderLine

      protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, String source, String version)
      create a VCF format header line
      Parameters:
      name - the name for this header line
      count - the count for this header line
      type - the type for this header line
      description - the description for this header line
      lineType - the header line type
      source - annotation source (case-insensitive, e.g. "dbsnp")
      version - exact version (e.g. "138")

    • VCFCompoundHeaderLine

      protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, VCFCompoundHeaderLine.SupportedHeaderLineType lineType, String source, String version)
      create a VCF format header line
      Parameters:
      name - the name for this header line
      count - the count type for this header line
      type - the type for this header line
      description - the description for this header line
      lineType - the header line type
      source - annotation source (case-insensitive, e.g. "dbsnp")
      version - exact version (e.g. "138")

    • VCFCompoundHeaderLine

      protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, VCFCompoundHeaderLine.SupportedHeaderLineType lineType)
      create a VCF format header line
      Parameters:
      line - the header line
      version - the VCF header version
      lineType - the header line type

  • Method Details

    • getID

      public String getID()
      Specified by:
      getID in interface VCFIDHeaderLine

    • getDescription

      public String getDescription()

    • getType

      public VCFHeaderLineType getType()

    • getCountType

      public VCFHeaderLineCount getCountType()

    • isFixedCount

      public boolean isFixedCount()

    • getCount

      public int getCount()

    • getSource

      public String getSource()

    • getVersion

      public String getVersion()

    • getCount

      public int getCount(VariantContext vc)
      Get the number of values expected for this header field, given the properties of VariantContext vc If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1 If the count is of type A, return vc.getNAlleles - 1 If the count is of type R, return vc.getNAlleles If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information at all, then implicitly assume diploid samples when computing G values. If the count is UNBOUNDED return -1
      Parameters:
      vc -
      Returns:

    • setNumberToUnbounded

      public void setNumberToUnbounded()

    • toStringEncoding

      protected String toStringEncoding()
      make a string representation of this header line
      Overrides:
      toStringEncoding in class VCFHeaderLine
      Returns:
      a string representation

    • equals

      public boolean equals(Object o)
      returns true if we're equal to another compound header line
      Overrides:
      equals in class VCFHeaderLine
      Parameters:
      o - a compound header line
      Returns:
      true if equal

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class VCFHeaderLine

    • equalsExcludingDescription

      public boolean equalsExcludingDescription(VCFCompoundHeaderLine other)

    • sameLineTypeAndName

      public boolean sameLineTypeAndName(VCFCompoundHeaderLine other)

    • setSource

      public void setSource(String source)
      Specify annotation source

      This value is optional starting with VCFv4.2.

      Parameters:
      source - annotation source (case-insensitive, e.g. "dbsnp")

    • setVersion

      public void setVersion(String version)
      Specify annotation version

      This value is optional starting with VCFv4.2.

      Parameters:
      version - exact version (e.g. "138")