Package vcf

Class VcfIt<E extends GTRec>

java.lang.Object
vcf.VcfIt<E>
Type Parameters:
E - the type parameter
All Implemented Interfaces:
FileIt<E>, SampleFileIt<E>, VcfFileIt<E>, Closeable, AutoCloseable, Iterator<E>
public class VcfIt<E extends GTRec> extends Object implements VcfFileIt<E>

Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.

Instances of class VcfIt are not thread-safe.

Methods of this class will terminate the Java Virtual Machine with an error message if an I/O error or file format error is detected.

  • Field Details

    • DEFAULT_BUFFER_SIZE

      public static final int DEFAULT_BUFFER_SIZE
      The default number of VCF records stored in a buffer.
      See Also:

    • TO_LOWMEM_GT_REC

      public static final TriFunction<VcfHeader,String,MarkerParser,GTRec> TO_LOWMEM_GT_REC
      A function mapping a string VCF record with GT format fields to a memory-efficient GTRec object. Phase status is stored per record. All genotypes are considered to be unphased if any genotype is unphased or if any allele is missing.

    • TO_BASIC_GT_REC

      public static final TriFunction<VcfHeader,String,MarkerParser,GTRec> TO_BASIC_GT_REC
      A function mapping a string VCF record to a BasicGTRec object. Phase status is stored per-genotype.

    • TO_VCF_REC

      public static final TriFunction<VcfHeader,String,MarkerParser,VcfRec> TO_VCF_REC
      A function mapping a string VCF record to a VcfRec object.

  • Method Details

    • head

      public static String[] head(String src, FileIt<String> it)
      Returns an array containing VCF meta-information lines, the VCF header line, and the first VCF data line. The returned array will contain all initial lines that begin with the '#' character and the next line.
      Parameters:
      src - a string describing the source of the VCF file
      it - an iterator that returns the lines of a VCF file
      Returns:
      an array containing VCF meta-information lines, the VCF header line, and the first VCF data line
      Throws:
      NullPointerException - if it == null
      IllegalArgumentException - if all lines returned by the iterator begin with the '#' character

    • create

      public static <R extends GTRec> VcfIt<R> create(FileIt<String> strIt, TriFunction<VcfHeader,String,MarkerParser,R> recMapper)
      Create and returns a new VcfIt instance from the specified objects.
      Type Parameters:
      R - the type returned by the returned VcfIt
      Parameters:
      strIt - an iterator that returns lines of a VCF file
      recMapper - a function mapping string VCF records to GTRec objects
      Returns:
      a new VcfIt instance
      Throws:
      IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
      NullPointerException - if strIt == null || mapFactory == null

    • create

      public static <R extends GTRec> VcfIt<R> create(FileIt<String> strIt, Filter<String> sampleFilter, Filter<Marker> markerFilter, TriFunction<VcfHeader,String,MarkerParser,R> recMapper)
      Create and returns a new VcfIt instance from the specified objects.
      Type Parameters:
      R - the type returned by the returned VcfIt
      Parameters:
      strIt - an iterator that returns lines of a VCF file
      sampleFilter - a sample filter or null
      markerFilter - a marker filter or null
      recMapper - a function mapping string VCF records to GTRec objects
      Returns:
      a new VcfIt instance
      Throws:
      IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
      NullPointerException - if strIt == null || mapFactory == null

    • create

      public static <R extends GTRec> VcfIt<R> create(FileIt<String> strIt, Filter<String> sampleFilter, Filter<Marker> markerFilter, TriFunction<VcfHeader,String,MarkerParser,R> recMapper, int bufferSize)
      Create and returns a new VcfIt instance from the specified objects.
      Type Parameters:
      R - the type returned by the returned VcfIt
      Parameters:
      strIt - an iterator that returns lines of a VCF file
      sampleFilter - a sample filter or null
      markerFilter - a marker filter or null
      recMapper - a function mapping string VCF records to GTRec objects
      bufferSize - the requested buffer size
      Returns:
      a new VcfIt instance
      Throws:
      IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
      IllegalArgumentException - if bufferSize < 1
      NullPointerException - if strIt == null || mapFactory == null

    • close

      public void close()
      Description copied from interface: FileIt
      Closes the input stream and releases any system resources that are associated with it. If the input stream is already closed then invoking this method has no effect.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface FileIt<E extends GTRec>

    • hasNext

      public boolean hasNext()
      Returns true if the iteration has more elements, and returns false otherwise.
      Specified by:
      hasNext in interface Iterator<E extends GTRec>
      Returns:
      true if the iteration has more elements

    • next

      public E next()
      Returns the next element in the iteration.
      Specified by:
      next in interface Iterator<E extends GTRec>
      Returns:
      the next element in the iteration
      Throws:
      NoSuchElementException - if the iteration has no more elements.

    • remove

      public void remove()
      The remove method is not supported by this iterator.
      Specified by:
      remove in interface Iterator<E extends GTRec>
      Throws:
      UnsupportedOperationException - if this method is invoked

    • file

      public File file()
      Description copied from interface: FileIt
      Returns the file from which the data are read, or null if the data are read from standard input or if the data source is unknown.
      Specified by:
      file in interface FileIt<E extends GTRec>
      Returns:
      the file from which the data are read, or null if the data are read from standard input or if the data source is unknown

    • samples

      public Samples samples()
      Description copied from interface: SampleFileIt
      Returns the list of samples.
      Specified by:
      samples in interface SampleFileIt<E extends GTRec>
      Returns:
      the list of samples

    • vcfHeader

      public VcfHeader vcfHeader()
      Description copied from interface: VcfFileIt
      Returns the VCF meta-information lines and header line
      Specified by:
      vcfHeader in interface VcfFileIt<E extends GTRec>
      Returns:
      the VCF meta-information lines and header line

    • toString

      public String toString()
      Description copied from interface: FileIt
      Returns a string representation of this. The exact details of the representation are unspecified and subject to change.
      Specified by:
      toString in interface FileIt<E extends GTRec>
      Overrides:
      toString in class Object
      Returns:
      a string representation of this