Package htsjdk.variant.vcf

Class VCFFileReader

java.lang.Object
htsjdk.variant.vcf.VCFFileReader
All Implemented Interfaces:
VCFReader, Closeable, AutoCloseable, Iterable<VariantContext>
public class VCFFileReader extends Object implements VCFReader
Simplified interface for reading from VCF/BCF files.

  • Constructor Details

    • VCFFileReader

      public VCFFileReader(File file)
      Constructs a VCFFileReader that requires the index to be present.

    • VCFFileReader

      public VCFFileReader(File file, File indexFile)
      Constructs a VCFFileReader with a specified index.

    • VCFFileReader

      public VCFFileReader(File file, boolean requireIndex)
      Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.

    • VCFFileReader

      public VCFFileReader(File file, File indexFile, boolean requireIndex)
      Allows construction of a VCFFileReader with a specified index file.

    • VCFFileReader

      public VCFFileReader(Path path)
      Constructs a VCFFileReader that requires the index to be present.

    • VCFFileReader

      public VCFFileReader(Path path, Path indexPath)
      Constructs a VCFFileReader with a specified index.

    • VCFFileReader

      public VCFFileReader(Path path, boolean requireIndex)
      Allows construction of a VCFFileReader that will or will not assert the presence of an index as desired.

    • VCFFileReader

      public VCFFileReader(Path path, Path indexPath, boolean requireIndex)
      Allows construction of a VCFFileReader with a specified index path.

  • Method Details

    • isBCF

      public static boolean isBCF(File file)
      Returns true if the given file appears to be a BCF file.

    • isBCF

      public static boolean isBCF(Path path)
      Returns true if the given path appears to be a BCF file.

    • getSequenceDictionary

      public static SAMSequenceDictionary getSequenceDictionary(File file)
      Returns the SAMSequenceDictionary from the provided VCF file.

    • getSequenceDictionary

      public static SAMSequenceDictionary getSequenceDictionary(Path path)
      Returns the SAMSequenceDictionary from the provided VCF file.

    • toIntervalList

      public static IntervalList toIntervalList(Path path)
      Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals
      Parameters:
      path - a VCF
      Returns:

    • toIntervalList

      public static IntervalList toIntervalList(Path path, boolean includeFiltered)

    • fromVcf

      @Deprecated public static IntervalList fromVcf(File file)
      Deprecated.
      since July 2018 use toIntervalList(Path) instead
      Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals
      Parameters:
      file - a VCF
      Returns:
      an IntervalList

    • fromVcf

      @Deprecated public static IntervalList fromVcf(File file, boolean includeFiltered)
      Deprecated.
      since July 2018 use toIntervalList(Path, boolean) instead
      Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists. if not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals
      Parameters:
      file -
      Returns:

    • toIntervalList

      public IntervalList toIntervalList()
      Converts the underlying VCFFileReader to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. If not, creates a name of the format 'interval-n' where n is a running number that increments on un-named intervals. Will use the "END" tag in the INFO field as the end of the interval (if exists).
      Returns:
      an IntervalList constructed from input vcf

    • toIntervalList

      public IntervalList toIntervalList(boolean includeFiltered)

    • fromVcf

      @Deprecated public static IntervalList fromVcf(VCFFileReader vcf)
      Deprecated.
      since July 2018 since use toIntervalList(VCFFileReader) instead
      Converts a vcf to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals. Will use a "END" tag in the INFO field as the end of the interval (if exists).
      Parameters:
      vcf - the vcfReader to be used for the conversion
      Returns:
      an IntervalList constructed from input vcf

    • toIntervalList

      public static IntervalList toIntervalList(VCFFileReader vcf)
      Converts a vcf to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals. Will use a "END" tag in the INFO field as the end of the interval (if exists).
      Parameters:
      vcf - the vcfReader to be used for the conversion
      Returns:
      an IntervalList constructed from input vcf

    • fromVcf

      @Deprecated public static IntervalList fromVcf(VCFFileReader vcf, boolean includeFiltered)
      Deprecated.
      since July 2018 since use toIntervalList(VCFFileReader, boolean) instead
      Converts a vcf to an IntervalList. The name field of the IntervalList is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals. Will use a "END" tag in the INFO field as the end of the interval (if exists).
      Parameters:
      vcf - the vcfReader to be used for the conversion
      Returns:
      an IntervalList constructed from input vcf

    • toIntervalList

      public static IntervalList toIntervalList(VCFFileReader vcf, boolean includeFiltered)
      Converts a VCFFileReader to an IntervalList. The name field of the Interval is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals. Will use a "END" tag in the INFO field as the end of the interval (if exists).
      Parameters:
      vcf - the vcfReader to be used for the conversion
      Returns:
      an IntervalList constructed from input vcf

    • toIntervals

      public static Iterator<Interval> toIntervals(VCFFileReader vcf, boolean includeFiltered)
      Converts a VCFFileReader to an Iterator<Interval> The name field of the Interval is taken from the ID field of the variant, if it exists. If not, creates a name of the format interval-n where n is a running number that increments only on un-named intervals. Will use a "END" tag in the INFO field as the end of the interval (if exists).
      Parameters:
      vcf - the vcfReader to be used for the conversion
      Returns:
      a Iterator constructed from input vcf

    • getHeader

      public VCFHeader getHeader()
      Returns the VCFHeader associated with this VCF/BCF file.
      Specified by:
      getHeader in interface VCFReader

    • getFileHeader

      public final VCFHeader getFileHeader()
      Synonym of getHeader()

    • iterator

      public CloseableIterator<VariantContext> iterator()
      Returns an iterator over all records in this VCF/BCF file.
      Specified by:
      iterator in interface Iterable<VariantContext>
      Specified by:
      iterator in interface VCFReader

    • query

      public CloseableIterator<VariantContext> query(String chrom, int start, int end)
      Queries for records overlapping the region specified. Note that this method requires VCF files with an associated index. If no index exists a TribbleException will be thrown.
      Specified by:
      query in interface VCFReader
      Parameters:
      chrom - the chomosome to query
      start - query interval start
      end - query interval end
      Returns:
      non-null iterator over VariantContexts

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable

    • isQueryable

      public boolean isQueryable()
      A method to check if the reader is query-able, i.e. if a call to query(String, int, int) can be successful
      Specified by:
      isQueryable in interface VCFReader
      Returns:
      true if the reader can be queried, i.e. if the underlying Tribble reader is queryable.