class HTS::Bam::Record

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

Defined in:

Constant Summary

SEQ_NT16_STR = "=ACMGRSVTWYHKDBN"

Constructors

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

Instance Method Summary

• #aux(str)
• #aux_char(str)
• #aux_float(str)
• #aux_int(str)

  Retrun Int64

• #aux_string(str)
• #base(n)

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

• #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.

• #clone
• #contig

  returns the mate chromosome or '' if not mapped.

• #duplicate?
• #endpos

  returns end position of the read.

• #finalize

  garbagew collection

• #flag

  returns a Flag object.

• #flag=(flag : Flag)
• #flag=(flag)
• #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
• #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>