class HTS::Bam::Record

• HTS::Bam::Record
• Reference
• Object

Defined in:

Constant Summary

SEQ_NT16_STR = "=ACMGRSVTWYHKDBN"

Constructors

• .new(header : Bam::Header, qname : String, flag : UInt16 | Int32, tid : Int32, pos : Int64, mapq : UInt8 | Int32, cigar_words : Array(UInt32), seq : String, qual : Array(UInt8), mtid : Int32 = -1, mpos : Int64 = 0_i64, isize : Int64 = 0_i64)

  Convenience constructor: build a record with core fields using bam_set1 - Coordinates are 0-based (as in BAM core) - CIGAR may be given as encoded words (Array(UInt32)) or SAM string - Qualities are Phred-scaled values (0..93), one per base

• .new(header : Bam::Header, qname : String, flag : UInt16 | Int32, rname : String, pos : Int64, mapq : UInt8 | Int32, cigar_str : String, seq : String, qual : Array(UInt8), mtid : Int32 = -1, mpos : Int64 = 0_i64, isize : Int64 = 0_i64)

  Overload: rname + CIGAR as String

• .new(header : Bam::Header, bam1_t : Pointer(HTS::LibHTS::Bam1T))
• .new(header : Bam::Header)

Instance Method Summary

• #aux

  Return Aux object for iteration over all auxiliary tags

• #aux_char(str) : Char | Nil
• #aux_float(str) : Float64 | Nil
• #aux_int(str) : Int64 | Nil

  Return Int64

• #aux_string(str) : String | Nil
• #base(n)

  return only the base of the requested index "i" of the query sequence.

• #base_mod : Bam::BaseMod

  Base modification accessor NOTE: Currently always returns a new BaseMod instance to avoid a finalizer cycle between Record and BaseMod.

• #base_qual(n)

  return only the base quality of the requested index "i" of the query sequence.

• #bin
• #bin=(bin)
• #chrom

  returns the chromosome or '' if not mapped.

• #cigar

  returns a Cigar object.

• #cigar_size : UInt32

  Returns the number of CIGAR operations in this record without allocating a Cigar object.

• #clone
• #contig

  returns the mate chromosome or '' if not mapped.

• #duplicate?
• #each_base(&)

  Iterate over query sequence bases without building a String.

• #each_cigar(& : Tuple(Char, UInt32) -> ) : self

  Iterate over CIGAR operations without allocating a Cigar object or copying the encoded CIGAR words out of the BAM record.

• #each_qual(&)

  Iterate over base qualities without building an Array.

• #endpos

  returns end position of the read.

• #finalize

  garbagew collection

• #flag

  returns a Flag object.

• #flag=(flag : Flag)
• #flag=(flag)
• #flag_value : UInt16
• #has_flag?(mask) : Bool
• #header : HTS::Bam::Header
• #insert_size

  insert size

• #insert_size=(isize)
• #isize
• #isize=(isize)
• #len
• #mapq

  mapping quality

• #mapq=(mapq)
• #mate_chrom

  returns the chromosome of the mate or '' if not mapped.

• #mate_contig
• #mate_pos

  returns 0-based mate position

• #mate_pos=(mpos)
• #mate_reverse?
• #mate_strand
• #mate_unmapped?
• #mpos
• #mpos=(mpos)
• #mtid

  returns the tid of the mate or -1 if not mapped.

• #mtid=(mtid)
• #paired?
• #pos

  returns 0-based start position.

• #pos=(pos)
• #proper_pair?
• #qcfail?
• #qlen
• #qname

  returns the query name.

• #qname=(name)
• #qual

  return the base qualities

• #qual_string

  Return base qualities as a Phred+33 QUAL string.

• #read1?
• #read2?
• #reverse?
• #rlen
• #secondary?
• #seq

  return the read sequence

• #sequence
• #strand
• #supplementary?
• #tid

  returns the tid of the record or -1 if not mapped.

• #tid=(tid)
• #to_s(io : IO)

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

• #to_unsafe : Pointer(HTS::LibHTS::Bam1T)
• #unmapped?

Constructor Detail

Instance Method Detail

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

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