Package vcf

Class VcfIt<E extends GTRec>

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

      Fields 
      Modifier and Type Field Description
      static int DEFAULT_BUFFER_SIZE
      The default number of VCF records stored in a buffer.
      static java.util.function.BiFunction<VcfHeader,​java.lang.String,​GTRec> TO_BASIC_GT_REC
      A function mapping a string VCF record with GT format fields to a GTRec object.
      static java.util.function.BiFunction<VcfHeader,​java.lang.String,​GTRec> TO_LOWMEM_GT_REC
      A function mapping a string VCF record with GT format fields to a memory-efficient GTRec object.
      static java.util.function.BiFunction<VcfHeader,​java.lang.String,​VcfRec> TO_VCF_REC
      A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Stops reading data elements and releases any system resources that are held by this object.
      static <R extends GTRec>
      VcfIt<R>      		 create​(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, Filter<Marker> markerFilter, java.util.function.BiFunction<VcfHeader,​java.lang.String,​R> recMapper)
      Create and returns a new VcfIt instance from the specified objects.
      static <R extends GTRec>
      VcfIt<R>      		 create​(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, Filter<Marker> markerFilter, java.util.function.BiFunction<VcfHeader,​java.lang.String,​R> recMapper, int bufferSize)
      Create and returns a new VcfIt instance from the specified objects.
      static <R extends GTRec>
      VcfIt<R>      		 create​(FileIt<java.lang.String> strIt, java.util.function.BiFunction<VcfHeader,​java.lang.String,​R> recMapper)
      Create and returns a new VcfIt instance from the specified objects.
      java.io.File file()
      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.
      boolean hasNext()
      Returns true if the iteration has more elements, and returns false otherwise.
      E next()
      Returns the next element in the iteration.
      void remove()
      The remove method is not supported by this iterator.
      Samples samples()
      Returns the list of samples.
      java.lang.String toString()
      Returns a string representation of this.

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.util.Iterator

        forEachRemaining

    • Field Detail

      • DEFAULT_BUFFER_SIZE

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

      • TO_LOWMEM_GT_REC

        public static final java.util.function.BiFunction<VcfHeader,​java.lang.String,​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 java.util.function.BiFunction<VcfHeader,​java.lang.String,​GTRec> TO_BASIC_GT_REC
        A function mapping a string VCF record with GT format fields to a GTRec object. Phase status is stored per-genotype.

      • TO_VCF_REC

        public static final java.util.function.BiFunction<VcfHeader,​java.lang.String,​VcfRec> TO_VCF_REC
        A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.

    • Method Detail

      • create

        public static <R extends GTRec> VcfIt<R> create​(FileIt<java.lang.String> strIt,
                                                java.util.function.BiFunction<VcfHeader,​java.lang.String,​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:
        java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
        java.lang.NullPointerException - if strIt == null || mapFactory == null

      • create

        public static <R extends GTRec> VcfIt<R> create​(FileIt<java.lang.String> strIt,
                                                Filter<java.lang.String> sampleFilter,
                                                Filter<Marker> markerFilter,
                                                java.util.function.BiFunction<VcfHeader,​java.lang.String,​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:
        java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
        java.lang.NullPointerException - if strIt == null || mapFactory == null

      • create

        public static <R extends GTRec> VcfIt<R> create​(FileIt<java.lang.String> strIt,
                                                Filter<java.lang.String> sampleFilter,
                                                Filter<Marker> markerFilter,
                                                java.util.function.BiFunction<VcfHeader,​java.lang.String,​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:
        java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt
        java.lang.IllegalArgumentException - if bufferSize < 1
        java.lang.NullPointerException - if strIt == null || mapFactory == null

      • close

        public void close()
        Description copied from interface: FileIt
        Stops reading data elements and releases any system resources that are held by this object. Buffered data elements may remain accessible via the hasNext() and next() methods after invoking close(). After invoking close(), further invocations of close() have no effect.
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface java.io.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 java.util.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 java.util.Iterator<E extends GTRec>
        Returns:
        the next element in the iteration
        Throws:
        java.util.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 java.util.Iterator<E extends GTRec>
        Throws:
        java.lang.UnsupportedOperationException - if this method is invoked

      • file

        public java.io.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

      • toString

        public java.lang.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 java.lang.Object
        Returns:
        a string representation of this