Type Members

1.  type Abundance = Long

   Internal type of abundance counts for k-mers.

   Internal type of abundance counts for k-mers. Even though this is a Long, some algorithms use 32-bit values, so overall only 32-bit counters are currently supported, bounded by the two values below.

2.  trait AdvancedMinimizerConfiguration extends MinimizerCLIConf

   Extra configuration options relating to advanced minimizer orderings

3.  type AnyMinSplitter = MinSplitter[MinimizerPriorities]
4.  class FastaOutputFormat[K, V] extends TextOutputFormat[K, V]
5.  trait HasInputReader extends AnyRef
6.  final case class IndexParams(bcSplit: Broadcast[AnyMinSplitter], buckets: Int, location: String) extends Product with Serializable

   Parameters for a k-mer index.

   Parameters for a k-mer index.

   bcSplit

   The broadcast splitter (minimizer scheme/ordering)

   buckets

   The number of buckets (Spark partitions) to partition the index into - NB, not the same as minimizer bins

   location

   The location (directory/prefix name) where the index is stored

7.  trait KmerKeyedIndex extends AnyRef

   Methods to support an index of key-value pairs with a fixed number of id columns (Longs) that contain an encoded k-mer.

8.  trait MinimizerCLIConf extends AnyRef

   Command-line configuration for minimizer schemes

9.  class MinimizerConfig extends AnyRef

   Configuration parameters for the construction of a minimizer ordering for k-mers.

10.  trait MinimizerFormats[C <: MinimizerCLIConf] extends AnyRef

    Management of the set of minimizer formats supported by an application.

    Management of the set of minimizer formats supported by an application. Allows for constructing a MinSplitter from a configuration, and for looking up SplitterFormat by id (string) or by class.

    C

    Supported configuration type

11.  type NTSeq = String

    Type of nucleotide sequences in human-readable form.

12.  final case class Path(path: String) extends MinimizerSource with Product with Serializable

    A file, or a directory containing multiple files with names like minimizers_{k}_{m}.txt, in which case the best file will be selected.

    A file, or a directory containing multiple files with names like minimizers_{k}_{m}.txt, in which case the best file will be selected. These files may specify an ordering.

    path

    the file, or directory to scan

13.  class RandomXORFormat extends SplitterFormat[RandomXOR]

    Computed minimizer format that applies an XOR mask.

14.  class Sampling extends AnyRef

    Routines for creating and managing frequency sampled minimizer orderings.

15.  final case class ScallopExitException(code: Int) extends Exception with Product with Serializable

    Thrown when Scallop wants to exit the application, for example because the configuration could not be parsed.

    Thrown when Scallop wants to exit the application, for example because the configuration could not be parsed.

    code

    exit code (as it would have been passed to System.exit)

16.  type SeqID = Int

    Type of Sequence IDs

17.  type SeqLocation = Long

    Type of locations on sequences

18.  type SeqTitle = String

    Type of Sequence titles/headers (as read from fasta/fastq files)

19.  class SparkConfiguration extends ScallopConf

    CLI configuration for a Spark-based application.

20.  trait SplitterFormat[P <: MinimizerPriorities] extends AnyRef

    Logic for persisting minimizer formats (ordering and parameters) to files.

21.  class StandardFormat extends SplitterFormat[MinTable]

    Minimizer format that uses a lookup table, storing the list of minimizers in a file.