Type Members

1.  class AnnotateBamWithUmis extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

2.  class CallDuplexConsensusReads extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

3.  class CallMolecularConsensusReads extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

4.  class CollectDuplexSeqMetrics extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

5.  class ConsensusCaller extends AnyRef

   Generic consensus caller class that can be used to produce consensus base calls and qualities from a pileup of raw base calls and qualities.

   Generic consensus caller class that can be used to produce consensus base calls and qualities from a pileup of raw base calls and qualities.

   The consensus caller sees the process of going from a DNA source molecule in its original, pristine, state to a sequenced base as having three phases each with their own distinct error profiles: 1) The phase whereby the source molecule is harvested (e.g. cells extracted and lysed) to the point where some kind of molecular identifier has been attached that will allow for identification of replicates that are generated from the same original source molecule. Errors in this phase will be present in all copies of the molecule that are prepared for sequencing (except where a second error reverts the change).

   2) Everything between phases 1 & 3! Generally including any sample preparation activities after a molecular identifier has been attached but prior to sequencing. Errors introduced in this phase will be present in some fraction of the molecules available at sequencing.

   3) Sequencing of the molecule (or clonal cluster of molecules) on a sequencer. E.g. the process of base-by-base resynthesis and sequencing on an Illumina sequencer _after_ cluster amplification. Errors in this phase are captured by the raw base quality scores from the sequencer.

6.  class ConsensusCallingIterator extends Iterator[SamRecord]

   An iterator that consumes from an incoming iterator of SAMRecords and generates consensus read SAMRecords using the supplied caller.

7.  class CorrectUmis extends FgBioTool with LazyLogging

   Annotations

   @ClpAnnotation()

8.  class DuplexConsensusCaller extends UmiConsensusCaller[DuplexConsensusRead] with LazyLogging

   Creates duplex consensus reads from SamRecords that have been grouped by their source molecule but not yet by source strand.

   Creates duplex consensus reads from SamRecords that have been grouped by their source molecule but not yet by source strand.

   Filters incoming bases by quality before building the duplex.

   Output reads and bases are constructed only if there is at least one read from each source molecule strand. Otherwise no filtering is performed.

   Note that a consequence of the above is that the output reads can be shorter than _some_ of the input reads if the input reads are of varying length; they will be the length at which there is coverage from both source strands.

9.  case class DuplexConsensusPerBaseValues (abStrand: Boolean, bases: String, depths: Array[Short], errors: Array[Short]) extends Product with Serializable

   A little class to store the per-base values for ab and ba-strand

10.  class ExtractUmisFromBam extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

11.  class FilterConsensusReads extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

12.  class GroupReadsByUmi extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

13.  class ReviewConsensusVariants extends FgBioTool with LazyLogging

    Annotations

    @ClpAnnotation()

14.  sealed trait Strategy extends EnumEntry

    The strategies implemented by GroupReadsByUmi to identify reads from the same source molecule.

15.  case class TagFamilySizeMetric (family_size: Int, count: Count, fraction: Proportion = 0, fraction_gt_or_eq_family_size: Proportion = 0) extends Metric with Product with Serializable

    Metrics produced by GroupReadsByUmi to describe the distribution of tag family sizes observed during grouping.

    Metrics produced by GroupReadsByUmi to describe the distribution of tag family sizes observed during grouping.

    family_size

    The family size, or number of templates/read-pairs belonging to the family.

    count

    The number of families (or source molecules) observed with family_size observations.

    fraction

    The fraction of all families of all sizes that have this specific family_size.

    fraction_gt_or_eq_family_size

    The fraction of all families that have >= family_size.

16.  trait UmiConsensusCaller [C <: SimpleRead] extends AnyRef

    A trait that can be mixed in by any consensus caller that works at the read level, mapping incoming SamRecords into consensus SamRecords.

    A trait that can be mixed in by any consensus caller that works at the read level, mapping incoming SamRecords into consensus SamRecords.

    C

    Internally, the type of lightweight consensus read that is used prior to rebuilding SamRecords.

17.  case class VanillaConsensusRead (id: String, bases: Array[Byte], quals: Array[Byte], depths: Array[Short], errors: Array[Short]) extends SimpleRead with Product with Serializable

    Stores information about a consensus read.

    Stores information about a consensus read. All four arrays are of equal length.

    Depths and errors that have values exceeding Short.MaxValue (32767) will be called to Short.MaxValue.

    bases

    the base calls of the consensus read

    quals

    the calculated phred-scaled quality scores of the bases

    depths

    the number of raw reads that contributed to the consensus call at each position

    errors

    the number of contributing raw reads that disagree with the final consensus base at each position

18.  class VanillaUmiConsensusCaller extends UmiConsensusCaller[VanillaConsensusRead] with LazyLogging

    Calls consensus reads by grouping consecutive reads with the same SAM tag.

    Calls consensus reads by grouping consecutive reads with the same SAM tag.

    Consecutive reads with the SAM tag are partitioned into fragments, first of pair, and second of pair reads, and a consensus read is created for each partition. A consensus read for a given partition may not be returned if any of the conditions are not met (ex. minimum number of reads, minimum mean consensus base quality, ...).

19.  case class VanillaUmiConsensusCallerOptions (tag: String = DefaultTag, errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, qualityTrim: Boolean = DefaultQualityTrim, minConsensusBaseQuality: PhredScore = DefaultMinConsensusBaseQuality, minReads: Int = DefaultMinReads, maxReads: Int = DefaultMaxReads, producePerBaseTags: Boolean = DefaultProducePerBaseTags) extends Product with Serializable

    Holds the parameters/options for consensus calling.