Package vcf

Class VcfHeader

  • public final class VcfHeader
extends java.lang.Object

    Class VcfHeader represents the Variant Call Format (VCF) meta-information lines and the Variant Call Format header line that precede the first Variant Call Format record.

    Instances of class VcfHeader are immutable.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String HEADER_PREFIX
      A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.

    • Constructor Summary

      Constructors 
      Constructor Description
      VcfHeader​(java.lang.String src, java.lang.String[] lines, boolean[] isDiploid)
      Returns a VCF header object for the specified VCF meta information lines and header line.
      VcfHeader​(java.lang.String src, java.lang.String[] lines, boolean[] isDiploid, Filter<java.lang.String> sampleFilter)
      Returns a VCF header object for the specified VCF meta information lines and header line.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      VcfMetaInfo metaInfoLine​(int index)
      Returns the specified VCF meta-information line.
      int nHeaderFields()
      Returns the number of fields in the VCF header line before sample exclusions.
      int nMetaInfoLines()
      Returns the number of VCF meta-information lines.
      int nSamples()
      Returns the number of samples after sample exclusions.
      int nUnfilteredSamples()
      Returns the number of samples before sample exclusions.
      java.lang.String[] sampleIds()
      Returns this.sample().ids().
      Samples samples()
      Return the list of samples after sample exclusions.
      java.lang.String src()
      Returns the source from which data are read.
      java.lang.String toString()
      Returns the VCF meta-information lines and the VCF header line after applying sample exclusions.
      int unfilteredSampleIndex​(int sample)
      Returns the index of the specified sample in the original list of samples before sample exclusions.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • HEADER_PREFIX

        public static final java.lang.String HEADER_PREFIX
        A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.
        See Also:
        Constant Field Values

    • Constructor Detail

      • VcfHeader

        public VcfHeader​(java.lang.String src,
                 java.lang.String[] lines,
                 boolean[] isDiploid)
        Returns a VCF header object for the specified VCF meta information lines and header line. The header line must be the last line in the specified lines array.
        Parameters:
        src - a string describing the source of the VCF file
        lines - the VCF meta-information and header lines
        isDiploid - a boolean array whose k-th value is true if the k-th sample is diploid, and is false if the k-th sample is haploid
        Throws:
        java.lang.IllegalArgumentException - if a format error is encountered in a meta-information line or header lines}
        java.lang.NullPointerException - if src==null || lines == null || isDiploid == nulle

      • VcfHeader

        public VcfHeader​(java.lang.String src,
                 java.lang.String[] lines,
                 boolean[] isDiploid,
                 Filter<java.lang.String> sampleFilter)
        Returns a VCF header object for the specified VCF meta information lines and header line. The header line must be the last line in the specified lines array.
        Parameters:
        src - a string describing the source of the VCF file
        lines - the VCF meta-information and header lines
        isDiploid - a boolean array whose k-th value is true if the k-th sample is diploid, and is false if the k-th sample is haploid
        sampleFilter - a sample filter
        Throws:
        java.lang.IllegalArgumentException - if a format error is encountered in a meta-information line or header lines}
        java.lang.NullPointerException - if src==null || lines == null || isDiploid == null

    • Method Detail

      • src

        public java.lang.String src()
        Returns the source from which data are read. The string representation of the source is undefined and subject to change.
        Returns:
        the source from which data are read

      • nMetaInfoLines

        public int nMetaInfoLines()
        Returns the number of VCF meta-information lines. VCF meta-information lines are lines that precede the VCF header line. A VCF meta-information line must begin with "##".
        Returns:
        the number of VCF meta-information lines

      • metaInfoLine

        public VcfMetaInfo metaInfoLine​(int index)
        Returns the specified VCF meta-information line.
        Parameters:
        index - a VCF meta-information line index
        Returns:
        the specified VCF meta-information line
        Throws:
        java.lang.IndexOutOfBoundsException - if index < 0 || index >= this.nMetaInfoLines()

      • nHeaderFields

        public int nHeaderFields()
        Returns the number of fields in the VCF header line before sample exclusions.
        Returns:
        the number of fields in the VCF header line before sample exclusions

      • nUnfilteredSamples

        public int nUnfilteredSamples()
        Returns the number of samples before sample exclusions.
        Returns:
        the number of samples before sample exclusions

      • unfilteredSampleIndex

        public int unfilteredSampleIndex​(int sample)
        Returns the index of the specified sample in the original list of samples before sample exclusions.
        Parameters:
        sample - a sample index
        Returns:
        the index of the specified sample in the original list of samples before sample exclusions
        Throws:
        java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.size()

      • nSamples

        public int nSamples()
        Returns the number of samples after sample exclusions.
        Returns:
        the number of samples after sample exclusions

      • samples

        public Samples samples()
        Return the list of samples after sample exclusions.
        Returns:
        the list of samples after sample exclusions

      • sampleIds

        public java.lang.String[] sampleIds()
        Returns this.sample().ids().
        Returns:
        this.sample().ids()

      • toString

        public java.lang.String toString()
        Returns the VCF meta-information lines and the VCF header line after applying sample exclusions.
        Overrides:
        toString in class java.lang.Object
        Returns:
        the VCF meta-information lines and the VCF header line after applying sample exclusions.