Type Members

1.  class AutoGenerateReadGroupsByName extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

2.  case class BaseCounts (a: Int, c: Int, g: Int, t: Int, n: Int) extends Product with Serializable

   Utility class to count the number of observation of each kind of base.

3.  case class BaseEntry (rec: SAMRecord, offset: Int) extends PileupEntry with Product with Serializable

   Pileup entry representing a match or mismatch.

4.  class ClipOverlappingReads extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

5.  case class DeletionEntry (rec: SAMRecord, offset: Int) extends PileupEntry with Product with Serializable

   Pileup entry representing a deletion.

6.  class ErrorRateByReadPosition extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

7.  case class ErrorRateByReadPositionMetric (read_number: Int, position: Int, bases_total: Long, errors: Long, error_rate: Double, a_to_c_error_rate: Double, a_to_g_error_rate: Double, a_to_t_error_rate: Double, c_to_a_error_rate: Double, c_to_g_error_rate: Double, c_to_t_error_rate: Double) extends Metric with Product with Serializable

   Gives the error rate and total number of bases observed for each position within the read.

   Gives the error rate and total number of bases observed for each position within the read.

   read_number

   the read number (ex. 0 for fragments, 1 for read one of a pair, 2 for read two of a pair)

   position

   the position or cycle within the read (1-based).

   bases_total

   the total number of bases observed at this position.

   errors

   the total number of errors or non-reference basecalls observed at this position

   error_rate

   the overall error rate at position

   a_to_c_error_rate

   the rate of A>C (and T>G) error at the position

   a_to_g_error_rate

   the rate of A>G (and T>C) error at the position

   a_to_t_error_rate

   the rate of A>T (and T>A) error at the position

   c_to_a_error_rate

   the rate of C>A (and G>T) error at the position

   c_to_g_error_rate

   the rate of C>G (and G>C) error at the position

   c_to_t_error_rate

   the rate of C>T (and G>A) error at the position

8.  class EstimatePoolingFractions extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

9.  class EstimateRnaSeqInsertSize extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

10.  class FilterBam extends FgBioTool with LazyLogging

    Program which takes in a BAM file and filters out all reads for templates that match one or more criteria.

    Program which takes in a BAM file and filters out all reads for templates that match one or more criteria. Designed to be used to filter out reads that might confuse variant callers and lead to false positive variant calls.

    Annotations

    @ClpAnnotation()

11.  class FindTechnicalReads extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

12.  case class InsertSizeMetric (pair_orientation: PairOrientation, read_pairs: Long = 0, mean: Double = 0, standard_deviation: Double = 0, median: Double = 0, min: Long = 0, max: Long = 0, median_absolute_deviation: Double = 0) extends Metric with Product with Serializable
13.  case class InsertionEntry (rec: SAMRecord, offset: Int) extends PileupEntry with Product with Serializable

    Pileup entry representing an insertion.

14.  case class Pileup [A <: PileupEntry](refName: String, refIndex: Int, pos: Int, pile: Seq[A]) extends Iterable[A] with Product with Serializable

    Represents a pileup of reads/bases at a single genomic location.

15.  class PileupBuilder extends AnyRef

    Class that provides methods to build and filter Pileups.

16.  sealed trait PileupEntry extends AnyRef

    Base trait for pileup entries that exposes the SAMRecord and the 0-based offset into the record's bases and qualities that is relevant to the pileup.

17.  case class PoolingFractionMetric (sample: String, variant_sites: Int, singletons: Int, estimated_fraction: Double, standard_error: Double, ci99_low: Double, ci99_high: Double) extends Metric with Product with Serializable

    Metric to report out the estimated fraction of a pooled sample that comes from a specific sample.

    Metric to report out the estimated fraction of a pooled sample that comes from a specific sample.

    sample

    the sample within the pool being reported on

    variant_sites

    how many sites were examined at which the reported sample is known to be variant

    singletons

    how many of the variant sites were sites at which only this sample was variant

    estimated_fraction

    the estimated fraction of the pool that comes from this sample

    standard_error

    the standard error of the estimated fraction

    ci99_low

    the lower bound of the 99% confidence interval for the estimated fraction

    ci99_high

    the upper bound of the 99% confidence interval for the estimated fraction

18.  class RandomizeBam extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

19.  class RemoveSamTags extends FgBioTool

    Annotations

    @ClpAnnotation()

20.  class SamRecordClipper extends AnyRef

    Provides a suite of methods for clipping (soft- and hard-) bases from the beginnings and ends of reads in various ways.

    Provides a suite of methods for clipping (soft- and hard-) bases from the beginnings and ends of reads in various ways. Cigar strings, bases, qualities and alignment positions are all correctly adjusted post-clipping.

    Note that there are several "flavours" of method:

    • Ones that work on the start and end of the read in whatever orientation the read is in, vs. working on the 5' or 3' end of the read
    • Ones that attempt to clip an additional N bases beyond any clipping already provided (clip[Start|End|5PrimeEnd|3PrimeEnd]OfAlignment) and ones that attempt to make it so that the read has N bases clipped, including any existing clipping (clip[Start|End|5PrimeEnd|3PrimeEnd]OfRead)
21.  class SetMateInformation extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

22.  case class Template (r1: Option[SAMRecord], r2: Option[SAMRecord], r1Supplementals: Seq[SAMRecord] = Nil, r2Supplementals: Seq[SAMRecord] = Nil, r1Secondaries: Seq[SAMRecord] = Nil, r2Secondaries: Seq[SAMRecord] = Nil) extends Product with Serializable

    Class that represents all reads from a template within a BAM file.

23.  class TrimPrimers extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

24.  class UpdateReadGroups extends FgBioTool with LazyLogging

    Updates one or more read groups.

    Updates one or more read groups.

    Annotations

    @ClpAnnotation()