Class: Sam

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(line = nil) ⇒ Sam

Returns a new instance of Sam.



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# File 'lib/sam.rb', line 5

def initialize(line=nil)
  @tags = {}
  parse_line(line) if line != nil
end

Instance Attribute Details

#chrom ⇒ Object

Returns the value of attribute chrom.



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# File 'lib/sam.rb', line 3

def chrom
  @chrom
end

#cigar ⇒ Object

Returns the value of attribute cigar.



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# File 'lib/sam.rb', line 3

def cigar
  @cigar
end

#flag ⇒ Object

Returns the value of attribute flag.



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# File 'lib/sam.rb', line 3

def flag
  @flag
end

#insert ⇒ Object

Returns the value of attribute insert.



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# File 'lib/sam.rb', line 3

def insert
  @insert
end

#mapq ⇒ Object

Returns the value of attribute mapq.



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# File 'lib/sam.rb', line 3

def mapq
  @mapq
end

#mchrom ⇒ Object

Returns the value of attribute mchrom.



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# File 'lib/sam.rb', line 3

def mchrom
  @mchrom
end

#mpos ⇒ Object

Returns the value of attribute mpos.



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# File 'lib/sam.rb', line 3

def mpos
  @mpos
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/sam.rb', line 3

def name
  @name
end

#pos ⇒ Object

Returns the value of attribute pos.



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# File 'lib/sam.rb', line 3

def pos
  @pos
end

#qual ⇒ Object

Returns the value of attribute qual.



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# File 'lib/sam.rb', line 3

def qual
  @qual
end

#seq ⇒ Object

Returns the value of attribute seq.



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# File 'lib/sam.rb', line 3

def seq
  @seq
end

#tags ⇒ Object

Returns the value of attribute tags.



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# File 'lib/sam.rb', line 3

def tags
  @tags
end

Instance Method Details

#parse_line(line) ⇒ Object 



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# File 'lib/sam.rb', line 10

def parse_line(line)
  return false if line[0] == "@"
  
  f = line.chomp.split("\t", -1)
  raise "SAM lines must have at least 11 fields (had #{f.size})" if f.size < 11

  # colnames = %w(1:name 2:flag 3:chr 4:pos 5:mapq 6:cigar 7:mchr 8:mpos 9:insrt 10:seq 11:qual)

  @name = f[0]
  @flag = int_or_raw(f[1])
  @chrom = f[2]
  @pos = int_or_neg1(f[3])
  @mapq = int_or_neg1(f[4])
  @cigar = f[5]
  @mchrom = f[6]
  @mpos = int_or_neg1(f[7])
  @insert = int_or_raw(f[8])
  @seq = f[9]
  @qual = f[10]

  @tags = {}
  i = 11
  while i < f.size
    tag = f[i]
    i += 1
    colon_index = tag.rindex(':') 
    raise line if f.rindex == nil
    key = tag[0, colon_index]
    value = int_or_raw(tag[colon_index + 1, tag.size - colon_index] || "")
    @tags[key] = value
  end

  return true;
end