Package model

Record Class Storage.Parameters

java.lang.Object
java.lang.Record
model.Storage.Parameters
Record Components:
minimalCoverage - The minimal coverage of a variant call to be accepted. Must be greater than or equal to 0. This ensures that only variant calls with sufficient read depth are considered.
minimalFrequency - The minimal frequency of a variant call to be accepted. Must be between 0.0 and 1.0, inclusive. This parameter filters out low-frequency variants that may be due to sequencing errors.
maskFiltered - Whether to mask filtered calls as ambiguous bases (N) or ignore them.
skipAnnotation - Whether to skip the SnpEff annotation process. If true, the annotation step is bypassed, which can save time if annotation is not required.
skipTyping - Whether to skip proteoform inference. If true, the inference of proteoforms (protein isoforms) is not performed, which can be useful for non-coding regions.
masked - A map associating contig names with sets of positions to exclude from storage. Cannot be null but can be empty. This allows specific genomic positions to be ignored during analysis.
Enclosing class:
Storage
public static record Storage.Parameters(int minimalCoverage, double minimalFrequency, boolean maskFiltered, boolean skipAnnotation, boolean skipTyping, Map<String,Set<Integer>> masked) extends Record
The parameters used for configuring the storage of variant data.

This record encapsulates various parameters that control the behavior of the storage system, including thresholds for coverage and frequency, as well as exclusions for specific positions and variants. These parameters are immutable once set.

  • Constructor Details

    • Parameters

      public Parameters(int minimalCoverage, double minimalFrequency, boolean maskFiltered, boolean skipAnnotation, boolean skipTyping, Map<String,Set<Integer>> masked)
      Creates an instance of a Parameters record class.
      Parameters:
      minimalCoverage - the value for the minimalCoverage record component
      minimalFrequency - the value for the minimalFrequency record component
      maskFiltered - the value for the maskFiltered record component
      skipAnnotation - the value for the skipAnnotation record component
      skipTyping - the value for the skipTyping record component
      masked - the value for the masked record component

  • Method Details

    • isPositionMasked

      public boolean isPositionMasked(String contig, int position)
      Whether position is excluded on contig.
      Parameters:
      contig - Contig (id) to check for exclusion.
      position - Position to check for exclusion.
      Returns:
      True if position on contig is excluded from analysis.

    • toString

      public final String toString()
      Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
      Specified by:
      toString in class Record
      Returns:
      a string representation of this object

    • hashCode

      public final int hashCode()
      Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
      Specified by:
      hashCode in class Record
      Returns:
      a hash code value for this object

    • equals

      public final boolean equals(Object o)
      Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. Reference components are compared with Objects::equals(Object,Object); primitive components are compared with '=='.
      Specified by:
      equals in class Record
      Parameters:
      o - the object with which to compare
      Returns:
      true if this object is the same as the o argument; false otherwise.

    • minimalCoverage

      public int minimalCoverage()
      Returns the value of the minimalCoverage record component.
      Returns:
      the value of the minimalCoverage record component

    • minimalFrequency

      public double minimalFrequency()
      Returns the value of the minimalFrequency record component.
      Returns:
      the value of the minimalFrequency record component

    • maskFiltered

      public boolean maskFiltered()
      Returns the value of the maskFiltered record component.
      Returns:
      the value of the maskFiltered record component

    • skipAnnotation

      public boolean skipAnnotation()
      Returns the value of the skipAnnotation record component.
      Returns:
      the value of the skipAnnotation record component

    • skipTyping

      public boolean skipTyping()
      Returns the value of the skipTyping record component.
      Returns:
      the value of the skipTyping record component

    • masked

      public Map<String,Set<Integer>> masked()
      Returns the value of the masked record component.
      Returns:
      the value of the masked record component