Class: Bio::DB::Alignment

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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Alignment

Returns a new instance of Alignment.



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# File 'lib/bio/db/sam.rb', line 555

def initialize
  ObjectSpace.define_finalizer(self,
  self.class.method(:finalize).to_proc)
end

Instance Attribute Details

#al ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def al
  @al
end

#calend ⇒ Object

Attributes pulled with the C library



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# File 'lib/bio/db/sam.rb', line 575

def calend
  @calend
end

#cigar ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def cigar
  @cigar
end

#failed_quality ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def failed_quality
  @failed_quality
end

#first_in_pair ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def first_in_pair
  @first_in_pair
end

#flag ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def flag
  @flag
end

#is_duplicate ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def is_duplicate
  @is_duplicate
end

#is_mapped ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def is_mapped
  @is_mapped
end

#is_paired ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def is_paired
  @is_paired
end

#isize ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def isize
  @isize
end

#mapq ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def mapq
  @mapq
end

#mate_strand ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def mate_strand
  @mate_strand
end

#mate_unmapped ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def mate_unmapped
  @mate_unmapped
end

#mpos ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def mpos
  @mpos
end

#mrnm ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def mrnm
  @mrnm
end

#pos ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def pos
  @pos
end

#primary ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def primary
  @primary
end

#qlen ⇒ Object

Attributes pulled with the C library



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# File 'lib/bio/db/sam.rb', line 575

def qlen
  @qlen
end

#qname ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def qname
  @qname
end

#qual ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def qual
  @qual
end

#query_strand ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def query_strand
  @query_strand
end

#query_unmapped ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def query_unmapped
  @query_unmapped
end

#rname ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def rname
  @rname
end

#samstr ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def samstr
  @samstr
end

#second_in_pair ⇒ Object

Attrobites frp, 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



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# File 'lib/bio/db/sam.rb', line 579

def second_in_pair
  @second_in_pair
end

#seq ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def seq
  @seq
end

#tags ⇒ Object

Attributes from the format



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# File 'lib/bio/db/sam.rb', line 573

def tags
  @tags
end

Class Method Details

.finalize(object_id) ⇒ Object 



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# File 'lib/bio/db/sam.rb', line 559

def Alignment.finalize(object_id)

  #           puts "Object #{object_id} dying at #{Time.new}"
  #             p  "?" . object_id.al
  #            p object_id.al
  LibC.free object_id.al
  LibC.free object_id.sam
  LibC.free object_id.calend
  LibC.free object_id.qlen

  LibC.free object_id.samstr
end

Instance Method Details

#sam=(sam) ⇒ Object 



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# File 'lib/bio/db/sam.rb', line 613

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


  #<QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> \
  #[<TAG>:<VTYPE>:<VALUE> [...]] 

end

#set(bam_alignment, header) ⇒ Object 



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# File 'lib/bio/db/sam.rb', line 581

def set(bam_alignment, header)
  #Create the FFI object
  @al = Bio::DB::SAM::Tools::Bam1T.new(bam_alignment) 

  #set the raw data
  tmp_str =  Bio::DB::SAM::Tools.bam_format1(header,al)
  #self.sam =  tmp_str
  #ObjectSpace.define_finalizer(self, proc {|id| puts "Finalizer one on #{id}" })
  self.sam = String.new(tmp_str)
  #LibC.free tmp_str
  #Set values calculated by libbam
  core = al[:core]
  cigar = al[:data][core[:l_qname]]#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname)) 
  @calend = Bio::DB::SAM::Tools.bam_calend(core,cigar)
  @qlen = Bio::DB::SAM::Tools.bam_cigar2qlen(core,cigar)

  #process the flags
  @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