class HTS::Bam::BaseMod

• HTS::Bam::BaseMod
• Reference
• Object

Overview

Base modification information from MM/ML tags View over a Record's MM/ML tags using htslib base-mod API

Included Modules

• Enumerable(HTS::Bam::BaseMod::Position)

Defined in:

Constant Summary

HTS_MOD_REPORT_UNCHECKED = 1_u32

Default flags for parsing base modifications via htslib HTS_MOD_REPORT_UNCHECKED = 1 (report unvalidated mods instead of failing)

Constructors

• .new(record : HTS::Bam::Record, auto_parse : Bool = true)

Instance Method Summary

• #[](position : Int32) : Position | Nil

  Array-style access to modifications at a query position

• #at_pos(position : Int32, max_mods : Int32 = 10) : Position | Nil

  Get modifications at a specific query position (0-based); returns nil if none

• #close
• #each(max_mods : Int32 = 10, &block : Position -> )

  Iterate over all positions with modifications

• #each_position(max_mods : Int32 = 10, &block : Position -> )

  Alias for clarity and parity with common terminology

• #ensure_parsed!(flags : UInt32 = HTS_MOD_REPORT_UNCHECKED)
• #finalize
• #modification_types : Array(Int32)

  List of modification codes (positive char codes or negative ChEBI)

• #parse(flags : UInt32 = HTS_MOD_REPORT_UNCHECKED) : Int32

  Parse MM/ML tags; flags per HTSlib (e.g., HTS_MOD_REPORT_UNCHECKED = 1) Default to reporting unchecked modifications so we see MM/ML content without strict validation.

• #parsed? : Bool
• #query_type(code : Int32 | String)

  Query info about a specific modification code

• #query_type_at(index : Int32)

  Query info about i-th modification type

• #record : HTS::Bam::Record
• #recorded_types : Array(Int32)

  Alias for #modification_types

• #to_a : Array(Position)

  Returns an Array with all the elements in the collection.

• #to_s(io : IO) : Nil

  Appends a short String representation of this object which includes its class name and its object address.

Constructor Detail

Instance Method Detail

(1..5).to_a # => [1, 2, 3, 4, 5]

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).to_s # => #<Person:0x10a199f20>