class HTS::Bam::Aux

• HTS::Bam::Aux
• Reference
• Object

Overview

Provides iteration over auxiliary tags in BAM records

This class enables efficient access to all auxiliary tags using HTSlib's bam_aux_first and bam_aux_next functions.

Usage examples:

Iterate over all tags

record.aux.each do |tag, value| puts "#{tag}: #{value}" end

Access specific tags with stable return types

as_score = record.aux.get_int("AS")

Defined in:

hts/bam/auxi.cr

Constant Summary

AUX_ARRAY_TYPE = 'B'.ord.to_u8

AUX_CHAR_TYPE = 'A'.ord.to_u8

AUX_FLOAT_ARRAY_TYPE = 'f'.ord.to_u8

AUX_FLOAT_TYPES = {'f'.ord.to_u8, 'd'.ord.to_u8}

AUX_INT_TYPES = {'c'.ord.to_u8, 'C'.ord.to_u8, 's'.ord.to_u8, 'S'.ord.to_u8, 'i'.ord.to_u8, 'I'.ord.to_u8}

AUX_STRING_TYPES = {'Z'.ord.to_u8, 'H'.ord.to_u8}

Constructors

• .new(bam1 : Pointer(LibHTS::Bam1T))

Instance Method Summary

• #each(&)

  Iterate over all auxiliary tags

• #each_with_type(&)

  Iterate over all auxiliary tags with original BAM type information.

• #get_char(tag : String) : Char | Nil

  Returns the character value for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-character type.

• #get_float(tag : String) : Float64 | Nil

  Returns the float value for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-float type.

• #get_float_array(tag : String) : Array(Float64) | Nil

  Returns the float array for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-float-array type.

• #get_int(tag : String) : Int64 | Nil

  Returns the integer value for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-integer type.

• #get_int_array(tag : String) : Array(Int64) | Nil

  Returns the integer array for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-integer-array type.

• #get_string(tag : String) : String | Nil

  Returns the string value for tag, nil when absent, and raises AuxTypeError when the tag exists with a non-string type.

• #to_s(io : IO) : Nil

  HTSlib sam_format_aux1 compliant output with original type information

• #update_array(tag : String, values : Array(Number), subtype : Char = 'i')
• #update_char(tag : String, value : Char)
• #update_double(tag : String, value : Number)
• #update_float(tag : String, value : Number)
• #update_hex(tag : String, value : String)
• #update_int(tag : String, value : Int)
• #update_int16(tag : String, value : Int)
• #update_int32(tag : String, value : Int)
• #update_int8(tag : String, value : Int)
• #update_string(tag : String, value : String)
• #update_uint16(tag : String, value : Int)
• #update_uint32(tag : String, value : Int)
• #update_uint8(tag : String, value : Int)

Constructor Detail

Instance Method Detail