Class: Bio::DB::Alignment

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/alignment.rb

Overview

Attrobites for the flag field (see chapter 2.2.2 of the sam file documentation) query_strand and mate_strand are true if they are forward. It is the opposite to the definition in the BAM format for clarity. primary is the negation of is_negative from the BAM format

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(sam_string) ⇒ Alignment

parses the SAM string into its constituents and set its attributes



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# File 'lib/bio/db/alignment.rb', line 24

def initialize(sam_string)
  s = sam_string.chomp.split("\t")
  @sam_string = sam_string
  @qname = s[0]
  @flag  = s[1].to_i
  @rname = s[2]
  @pos   = s[3].to_i
  @mapq  = s[4].to_i
  @cigar = s[5]
  @mrnm  = s[6]
  @mpos  = s[7].to_i
  @isize = s[8].to_i
  @seq   = s[9]
  @qual =  s[10]
  @tags = {} 
  11.upto(s.size-1) {|n| 
    t = Bio::DB::Tag.new 
    t.set(s[n])
    tags[t.tag] = t
  }    

  @is_paired  = (@flag & 0x0001) > 0
  @is_mapped             = @flag & 0x0002 > 0
  @query_unmapped        = @flag & 0x0004 > 0
  @mate_unmapped         = @flag & 0x0008 > 0
  @query_strand          = !(@flag & 0x0010 > 0)
  @mate_strand           = !(@flag & 0x0020 > 0)
  @first_in_pair         = @flag & 0x0040 > 0
  @second_in_pair        = @flag & 0x0080 > 0
  @primary               = !(@flag & 0x0100 > 0)
  @failed_quality        = @flag & 0x0200 > 0
  @is_duplicate          = @flag & 0x0400 > 0

end

Instance Attribute Details

#al ⇒ Object

Returns the value of attribute al.



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# File 'lib/bio/db/alignment.rb', line 19

def al
  @al
end

#calend ⇒ Object

Returns the value of attribute calend.



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# File 'lib/bio/db/alignment.rb', line 19

def calend
  @calend
end

#cigar ⇒ Object

Returns the value of attribute cigar.



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# File 'lib/bio/db/alignment.rb', line 19

def cigar
  @cigar
end

#failed_quality ⇒ Object

Returns the value of attribute failed_quality.



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# File 'lib/bio/db/alignment.rb', line 21

def failed_quality
  @failed_quality
end

#first_in_pair ⇒ Object

Returns the value of attribute first_in_pair.



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# File 'lib/bio/db/alignment.rb', line 21

def first_in_pair
  @first_in_pair
end

#flag ⇒ Object

Returns the value of attribute flag.



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# File 'lib/bio/db/alignment.rb', line 19

def flag
  @flag
end

#is_duplicate ⇒ Object

Returns the value of attribute is_duplicate.



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# File 'lib/bio/db/alignment.rb', line 21

def is_duplicate
  @is_duplicate
end

#is_mapped ⇒ Object

Returns the value of attribute is_mapped.



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# File 'lib/bio/db/alignment.rb', line 21

def is_mapped
  @is_mapped
end

#is_paired ⇒ Object

Returns the value of attribute is_paired.



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# File 'lib/bio/db/alignment.rb', line 21

def is_paired
  @is_paired
end

#isize ⇒ Object

Returns the value of attribute isize.



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# File 'lib/bio/db/alignment.rb', line 19

def isize
  @isize
end

#mapq ⇒ Object

Returns the value of attribute mapq.



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# File 'lib/bio/db/alignment.rb', line 19

def mapq
  @mapq
end

#mate_strand ⇒ Object

Returns the value of attribute mate_strand.



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# File 'lib/bio/db/alignment.rb', line 21

def mate_strand
  @mate_strand
end

#mate_unmapped ⇒ Object

Returns the value of attribute mate_unmapped.



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# File 'lib/bio/db/alignment.rb', line 21

def mate_unmapped
  @mate_unmapped
end

#mpos ⇒ Object

Returns the value of attribute mpos.



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# File 'lib/bio/db/alignment.rb', line 19

def mpos
  @mpos
end

#mrnm ⇒ Object

Returns the value of attribute mrnm.



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# File 'lib/bio/db/alignment.rb', line 19

def mrnm
  @mrnm
end

#pos ⇒ Object

Returns the value of attribute pos.



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# File 'lib/bio/db/alignment.rb', line 19

def pos
  @pos
end

#primary ⇒ Object

Returns the value of attribute primary.



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# File 'lib/bio/db/alignment.rb', line 21

def primary
  @primary
end

#qlen ⇒ Object

Returns the value of attribute qlen.



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# File 'lib/bio/db/alignment.rb', line 19

def qlen
  @qlen
end

#qname ⇒ Object

Returns the value of attribute qname.



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# File 'lib/bio/db/alignment.rb', line 19

def qname
  @qname
end

#qual ⇒ Object

Returns the value of attribute qual.



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# File 'lib/bio/db/alignment.rb', line 19

def qual
  @qual
end

#query_strand ⇒ Object

Returns the value of attribute query_strand.



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# File 'lib/bio/db/alignment.rb', line 21

def query_strand
  @query_strand
end

#query_unmapped ⇒ Object

Returns the value of attribute query_unmapped.



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# File 'lib/bio/db/alignment.rb', line 21

def query_unmapped
  @query_unmapped
end

#rname ⇒ Object

Returns the value of attribute rname.



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# File 'lib/bio/db/alignment.rb', line 19

def rname
  @rname
end

#sam_string ⇒ Object

Returns the value of attribute sam_string.



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# File 'lib/bio/db/alignment.rb', line 21

def sam_string
  @sam_string
end

#samstr ⇒ Object

Returns the value of attribute samstr.



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# File 'lib/bio/db/alignment.rb', line 19

def samstr
  @samstr
end

#second_in_pair ⇒ Object

Returns the value of attribute second_in_pair.



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# File 'lib/bio/db/alignment.rb', line 21

def second_in_pair
  @second_in_pair
end

#seq ⇒ Object

Returns the value of attribute seq.



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# File 'lib/bio/db/alignment.rb', line 19

def seq
  @seq
end

#tags ⇒ Object

Returns the value of attribute tags.



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# File 'lib/bio/db/alignment.rb', line 19

def tags
  @tags
end

Instance Method Details

#to_fastq ⇒ Object 



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# File 'lib/bio/db/alignment.rb', line 59

def to_fastq
  ["@#{qname}",seq, "+",qual].join "\n"
end