Constructor Detail

• BedEntry

  BedEntry(String chrom, Integer start, Integer end, String rest)

Method Detail

• compareTo

   Integer compareTo(BedEntry other)

• unpack

   final ExtendedBedEntry unpack(Byte fieldsNumber, Boolean parseExtraFields, Character delimiter, Boolean omitEmptyStrings)

  Unpacks a basic bed3 BedEntry into a bedN+ ExtendedBedEntry.

  Correctly parses the typed BED fields (such as score, color or blockSizes). Extra (non-standard) fields, if any (and if parseExtraFields is enabled) are stored in ExtendedBedEntry.extraFields property as a String array (null if no extra fields or parseExtraFields is disabled).

  Parameters:

  fieldsNumber - Expected regular BED format fields number to parse (3..

  parseExtraFields - Whether to parse or discard the BED+ format extra fields.

  delimiter - Custom delimiter for malformed data

  omitEmptyStrings - Treat several consecutive separators as one

• unpack

  @Deprecated(message = "use parseExtraFields instead of extraFieldsNumber", replaceWith = @ReplaceWith(imports = {}, expression = "unpack(fieldsNumber, extraFieldsNumber != 0, delimiter, omitEmptyStrings)")) final ExtendedBedEntry unpack(Byte fieldsNumber, Integer extraFieldsNumber, Character delimiter, Boolean omitEmptyStrings)

• component1

   final String component1()

• component2

   final Integer component2()

• component3

   final Integer component3()

• component4

   final String component4()

• copy

   final BedEntry copy(String chrom, Integer start, Integer end, String rest)

• getChrom

   final String getChrom()

  Chromosome name, e.g. "chr9".

• getStart

   final Integer getStart()

  0-based start offset (inclusive).

• getEnd

   final Integer getEnd()

  0-based end offset (exclusive).

• getRest

   final String getRest()

  Tab-separated string of additional BED values.