Type Members

1.  class DnaFoldPrediction extends AnyRef

2.  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.

3.  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.

4.  case class IndexMetric (index: String, source: String, min_mismatches: Int, indices_at_min_mismatches: Count, gc: Proportion, 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

   Output produced by PickLongIndices to describe the set of molecular indices picked by the program.

   Output produced by PickLongIndices to describe the set of molecular indices picked by the program.

   index

   The sequence of the molecular index (i.e. the set of bases).

   source

   The source of the sequence - either existing for indices provided to the program of novel for indices generated by the program.

   min_mismatches

   The smallest number of mismatches to any other reported molecular index.

   indices_at_min_mismatches

   The number of other reported molecular indices with min_mismatches differences to this index.

   gc

   The fraction of the sequence composed of G and C bases.

   longest_homopolymer

   The length of the longest homopolymer within the index sequence.

   worst_structure_seq

   The sequence (including adapter plus index) that generated the worst (lowest energy) structure for this index.

   worst_structure_dbn

   The lowest energy structure in dot-bracket notation.

   worst_structure_delta_g

   The deltaG of the lowest energy structure.

5.  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.

6.  trait Metric extends Product with Iterable[(String, String)]

   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.

7.  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()

8.  class PickLongIndices extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

9.  case class ProgressLogger (logger: Logger, noun: String = "records", verb: String = "processed", unit: Int = 1000 * 1000) extends AbstractProgressLogger with Product with Serializable

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

10.  case class ReadSegment (offset: Int, length: Option[Int], kind: SegmentType) extends Product with Serializable

    Encapsulates all the information about a segment within a read structure.

    Encapsulates all the information about a segment within a read structure. A segment can either have a definite length, in which case length must be Some(Int), or an indefinite length (can be any length, 0 or more) in which case length must be None.

11.  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.

12.  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, ...).

13.  case class SampleBarcodeMetric (barcode_name: String = "", library_name: String = "", barcode: String = "", templates: Count = 0, pf_templates: Count = 0, perfect_matches: Count = 0, pf_perfect_matches: Count = 0, one_mismatch_matches: Count = 0, pf_one_mismatch_matches: Count = 0, fraction_matches: Proportion = 0d, ratio_this_barcode_to_best_barcode: Proportion = 0d, pf_fraction_matches: Proportion = 0d, pf_ratio_this_barcode_to_best_barcode: Proportion = 0d, pf_normalized_matches: Proportion = 0d) extends Metric with Product with Serializable

    Metrics for matching templates to sample barcodes primarily used in com.fulcrumgenomics.fastq.DemuxFastqs.

    Metrics for matching templates to sample barcodes primarily used in com.fulcrumgenomics.fastq.DemuxFastqs.

    The number of templates will match the number of reads for an Illumina single-end sequencing run, while the number of templates will be half the number of reads for an Illumina paired-end sequencing run (i.e. R1 & R2 observe the same template).

    barcode_name

    the name for the sample barcode, typically the sample name from the SampleSheet.

    library_name

    the name of the library, typically the library identifier from the SampleSheet.

    barcode

    the sample barcode bases. Dual index barcodes will have two sample barcode sequences delimited by a dash.

    templates

    the total number of templates matching the given barcode.

    pf_templates

    the total number of pass-filter templates matching the given barcode.

    perfect_matches

    the number of templates that match perfectly the given barcode.

    pf_perfect_matches

    the number of pass-filter templates that match perfectly the given barcode.

    one_mismatch_matches

    the number of pass-filter templates that match the given barcode with exactly one mismatch.

    pf_one_mismatch_matches

    the number of pass-filter templates that match the given barcode with exactly one mismatch.

    fraction_matches

    the fraction of all templates that match the given barcode.

    ratio_this_barcode_to_best_barcode

    the rate of all templates matching this barcode to all template reads matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more unmatched templates than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes.

    pf_fraction_matches

    the fraction of all pass-filter templates that match the given barcode.

    pf_ratio_this_barcode_to_best_barcode

    the rate of all pass-filter templates matching this barcode to all templates matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more unmatched templates than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes.

    pf_normalized_matches

    The "normalized" matches to each barcode. This is calculated as the number of pass-filter templates matching this barcode over the mean of all pass-filter templates matching any barcode (excluding unmatched). If all barcodes are represented equally this will be 1.

14.  sealed abstract class SegmentType extends AnyRef

    Sealed class hierarchy for the types of segments that can show up in a read structure.

15.  class Sorter [A, B <: Ordered[B]] extends Iterable[A] with Writer[A]

    An implementation of a disk-backed sorting system.

    An implementation of a disk-backed sorting system. The implementation requires two things:

    1. An implementation of Codec that can serialize and deserialize objects 2. A function that creates a Ordered key object for each object being sorted

    Both must be thread-safe as they may be invoked across threads without external synchronization