Class: HTS::Bam::Record

Inherits:
Object
  • Object
show all
Defined in:
lib/hts/bam/record.rb

Overview

A class for working with alignment records.

Constant Summary collapse

SEQ_NT16_STR = 
"=ACMGRSVTWYHKDBN"

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(bam1_t, header) ⇒ Record

Returns a new instance of Record.



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# File 'lib/hts/bam/record.rb', line 15

def initialize(bam1_t, header)
  @bam1 = bam1_t
  @header = header
end

Instance Attribute Details

#header ⇒ Object (readonly)

Returns the value of attribute header.



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# File 'lib/hts/bam/record.rb', line 13

def header
  @header
end

Instance Method Details

#aux(key = nil) ⇒ Object

retruns the auxillary fields.



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# File 'lib/hts/bam/record.rb', line 209

def aux(key = nil)
  aux = Aux.new(self)
  if key
    aux.get(key)
  else
    aux
  end
end

#base(n) ⇒ Object

return only the base of the requested index “i” of the query sequence.



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# File 'lib/hts/bam/record.rb', line 169

def base(n)
  n += @bam1[:core][:l_qseq] if n < 0
  return "." if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base(-1000)

  r = LibHTS.bam_get_seq(@bam1)
  SEQ_NT16_STR[LibHTS.bam_seqi(r, n)]
end

#base_qual(n) ⇒ Object

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



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# File 'lib/hts/bam/record.rb', line 184

def base_qual(n)
  n += @bam1[:core][:l_qseq] if n < 0
  return 0 if (n >= @bam1[:core][:l_qseq]) || (n < 0) # eg. base_qual(-1000)

  q_ptr = LibHTS.bam_get_qual(@bam1)
  q_ptr.get_uint8(n)
end

#bin ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 77

def bin
  @bam1[:core][:bin]
end

#bin=(bin) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 81

def bin=(bin)
  @bam1[:core][:bin] = bin
end

#chrom ⇒ Object Also known as: contig

returns the chromosome or ” if not mapped.



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# File 'lib/hts/bam/record.rb', line 91

def chrom
  return "" if tid == -1

  LibHTS.sam_hdr_tid2name(@header, tid)
end

#cigar ⇒ Object

returns a ‘Cigar` object.



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# File 'lib/hts/bam/record.rb', line 135

def cigar
  Cigar.new(LibHTS.bam_get_cigar(@bam1), @bam1[:core][:n_cigar])
end

#endpos ⇒ Object

returns end position of the read.



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# File 'lib/hts/bam/record.rb', line 86

def endpos
  LibHTS.bam_endpos @bam1
end

#flag ⇒ Object

returns a ‘Flag` object.



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# File 'lib/hts/bam/record.rb', line 193

def flag
  Flag.new(@bam1[:core][:flag])
end

#flag=(flag) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 197

def flag=(flag)
  case flag
  when Integer
    @bam1[:core][:flag] = flag
  when Flag
    @bam1[:core][:flag] = flag.value
  else
    raise "Invalid flag type: #{flag.class}"
  end
end

#insert_size ⇒ Object Also known as: isize

insert size



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# File 'lib/hts/bam/record.rb', line 114

def insert_size
  @bam1[:core][:isize]
end

#insert_size=(isize) ⇒ Object Also known as: isize= 



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# File 'lib/hts/bam/record.rb', line 118

def insert_size=(isize)
  @bam1[:core][:isize] = isize
end

#len ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 164

def len
  @bam1[:core][:l_qseq]
end

#mapq ⇒ Object

mapping quality



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# File 'lib/hts/bam/record.rb', line 126

def mapq
  @bam1[:core][:qual]
end

#mapq=(mapq) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 130

def mapq=(mapq)
  @bam1[:core][:qual] = mapq
end

#mate_chrom ⇒ Object Also known as: mate_contig

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



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# File 'lib/hts/bam/record.rb', line 100

def mate_chrom
  return "" if mtid == -1

  LibHTS.sam_hdr_tid2name(@header, mtid)
end

#mate_pos ⇒ Object Also known as: mpos

returns 0-based mate position



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# File 'lib/hts/bam/record.rb', line 66

def mate_pos
  @bam1[:core][:mpos]
end

#mate_pos=(mpos) ⇒ Object Also known as: mpos= 



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# File 'lib/hts/bam/record.rb', line 70

def mate_pos=(mpos)
  @bam1[:core][:mpos] = mpos
end

#mtid ⇒ Object

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



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# File 'lib/hts/bam/record.rb', line 48

def mtid
  @bam1[:core][:mtid]
end

#mtid=(mtid) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 52

def mtid=(mtid)
  @bam1[:core][:mtid] = mtid
end

#pos ⇒ Object

returns 0-based start position.



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# File 'lib/hts/bam/record.rb', line 57

def pos
  @bam1[:core][:pos]
end

#pos=(pos) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 61

def pos=(pos)
  @bam1[:core][:pos] = pos
end

#qlen ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 139

def qlen
  LibHTS.bam_cigar2qlen(
    @bam1[:core][:n_cigar],
    LibHTS.bam_get_cigar(@bam1)
  )
end

#qname ⇒ Object

returns the query name.



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# File 'lib/hts/bam/record.rb', line 29

def qname
  LibHTS.bam_get_qname(@bam1).read_string
end

#qual ⇒ Object

return the base qualities



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# File 'lib/hts/bam/record.rb', line 178

def qual
  q_ptr = LibHTS.bam_get_qual(@bam1)
  q_ptr.read_array_of_uint8(@bam1[:core][:l_qseq])
end

#rlen ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 146

def rlen
  LibHTS.bam_cigar2rlen(
    @bam1[:core][:n_cigar],
    LibHTS.bam_get_cigar(@bam1)
  )
end

#seq ⇒ Object Also known as: sequence

return the read sequence



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# File 'lib/hts/bam/record.rb', line 154

def seq
  r = LibHTS.bam_get_seq(@bam1)
  seq = String.new
  (@bam1[:core][:l_qseq]).times do |i|
    seq << SEQ_NT16_STR[LibHTS.bam_seqi(r, i)]
  end
  seq
end

#strand ⇒ Object

Get strand information.



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# File 'lib/hts/bam/record.rb', line 109

def strand
  LibHTS.bam_is_rev(@bam1) ? "-" : "+"
end

#struct ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 20

def struct
  @bam1
end

#tid ⇒ Object

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



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# File 'lib/hts/bam/record.rb', line 39

def tid
  @bam1[:core][:tid]
end

#tid=(tid) ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 43

def tid=(tid)
  @bam1[:core][:tid] = tid
end

#to_ptr ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 24

def to_ptr
  @bam1.to_ptr
end

#to_s ⇒ Object 



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# File 'lib/hts/bam/record.rb', line 233

def to_s
  kstr = LibHTS::KString.new
  raise "Failed to format bam record" if LibHTS.sam_format1(@header.struct, @bam1, kstr) == -1

  kstr[:s]
end