Type Members

1.  class BetterBufferedIterator [A] extends BufferedIterator[A]

   A better buffered iterator that provides implementations of takeWhile and dropWhile that don't discard extra values.

2.  class DelimitedDataParser extends Iterator[Row] with LazyLogging

   A parser for files of text columns delimited by some character (e.g.

   A parser for files of text columns delimited by some character (e.g. tab-delimited or csv).

3.  class DnaFoldPrediction extends AnyRef

4.  class DnaFoldPredictor extends AnyRef

   Class that wraps ViennaRNAs RNAFold utility which can be used to estimate the minimum free energy secondary structure of DNA and RNA molecules.

   Class that wraps ViennaRNAs RNAFold utility which can be used to estimate the minimum free energy secondary structure of DNA and RNA molecules. When constructed a background process is started running RNAFold, calls to predict() then pipe input and output through RNAFold.

5.  trait GenomicSpan extends Locatable

   A simple trait that extends htsjdk.samtools.util.Locatable but provides a few easier to use methods for getting the location.

6.  case class IndexMetric (index: String, source: String, min_mismatches: Int, indices_at_min_mismatches: Int, gc: Double, longest_homopolymer: Int, worst_structure_seq: Option[String], worst_structure_dbn: Option[String], worst_structure_delta_g: Option[Double]) extends Metric with Product with Serializable

   A Metric class for information about each picked index.

7.  class Io extends IoUtil

   Provides common IO utility methods.

   Provides common IO utility methods. Can be instantiated to create a custom factory, or the companion object can be used as a singleton version.

8.  trait Metric extends Product

   Base trait for metrics.

   Base trait for metrics.

   All classes extending this class should be a case class. By convention, all fields should be lower case with words separated by underscores.

9.  case class MolecularBarcode (offset: Int, length: Int, symbol: Char = 'M') extends ReadSegment with Product with Serializable

   Bases used to identify the source molecule

10.  class NumericCounter [T] extends SimpleCounter[T]

    Super-simple class for counting occurrences of any [Numeric].

    Super-simple class for counting occurrences of any [Numeric]. Will return zero for any item that has not been counted yet. Implements some useful methods to compute statistics when the objects being counted are numeric types.

11.  class PickIlluminaIndices extends FgBioTool

    Program for picking sets of indices of arbitrary length that meet certain constraints and attempt to maximize the edit distance between all members of the set picked.

    Program for picking sets of indices of arbitrary length that meet certain constraints and attempt to maximize the edit distance between all members of the set picked.

    Annotations

    @ClpAnnotation()

12.  class PickLongIndices extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

13.  class ProgressLogger extends AbstractProgressLogger

    A subclass of HTSJDK's progress logger that uses fgbio's logging system.

14.  sealed trait ReadSegment extends AnyRef

    Base for all types of segments of a read

15.  class ReadStructure extends Seq[ReadSegment]

    Describes the structure of a give read.

    Describes the structure of a give read. A read contains one or more read segments. A read segment describes a contiguous stretch of bases of the same type (ex. template bases) of some length and some offset from the start of the read.

16.  class RefFlatSource extends Iterable[Gene] with Closeable with LazyLogging

    Reads gene annotation information from a RefFlat file.

    Reads gene annotation information from a RefFlat file.

    Skips genes on unrecognized chromosomes if a sequence dictionary is provided.

    The format is described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat

    A Picard-style header is also supported (GENE_NAME, TRANSCRIPT_NAME, ...).

17.  class Row extends AnyRef

    Represents a row of parsed data.

    Represents a row of parsed data. Provides methods for accessing values in a type-safe way either via apply() methods for non-optional fields or via get for optional fields.

18.  case class SampleBarcode (offset: Int, length: Int, symbol: Char = 'B') extends ReadSegment with Product with Serializable

    Bases used to identify the sample

19.  case class SampleBarcodeMetric (barcode_name: String = "", library_name: String = "", barcode: String = "", reads: Int = 0, pf_reads: Int = 0, perfect_matches: Int = 0, pf_perfect_matches: Int = 0, one_mismatch_matches: Int = 0, pf_one_mismatch_matches: Int = 0, pct_matches: Double = 0d, ratio_this_barcode_to_best_barcode_pct: Double = 0d, pf_pct_matches: Double = 0d, pf_ratio_this_barcode_to_best_barcode_pct: Double = 0d, pf_normalized_matches: Double = 0d) extends Metric with Product with Serializable

    Metrics for matching reads to sample barcodes.

20.  class SimpleCounter [T] extends Iterable[(T, Long)]

    Super-simple class for counting occurrences of any kind of object.

    Super-simple class for counting occurrences of any kind of object. Will return zero for any item that has not been counted yet.

21.  case class Skip (offset: Int, length: Int, symbol: Char = 'S') extends ReadSegment with Product with Serializable

    Bases to ignore

22.  case class Template (offset: Int, length: Int, symbol: Char = 'T') extends ReadSegment with Product with Serializable

    Bases from the template