bettersam 0.0.1.alpha

data/lib/bettersam.rb

@@ -0,0 +1,135 @@
+class BetterSam
+
+  # meanings of SAM flag components, with index i
+  # being one more than the exponent 2 must be raised to to get the
+  # value (i.e. value = 2^(i+1))
+  $flags = [
+    nil,
+    0x1,  #    1. read paired 
+    0x2,  #    2. read mapped in proper pair (i.e. with acceptable insert size)
+    0x4,  #    3. read unmapped
+    0x8,  #    4. mate unmapped
+    0x10,  #   5. read reverse strand
+    0x20,  #   6. mate reverse strand
+    0x40,  #   7. first in pair
+    0x80,  #   8. second in pair
+    0x100,  #  9. not primary alignment
+    0x200,  #  10. read fails platform/vendor quality checks
+    0x400]  #  11. read is PCR or optical duplicate
+
+public
+  attr_accessor :name, :flag, :chrom, :pos, :mapq, :cigar, :mchrom, :mpos, :insert, :seq, :qual, :tags
+
+  def initialize(line=nil)
+    @tags = {}
+    parse_line(line) unless line.nil?
+  end
+
+  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
+
+  # flag parsing convenience methods
+
+  def read_paired?
+    @flag & $flags[1] != 0
+  end
+
+  def read_properly_paired?
+    @flag & $flags[2] != 0
+  end
+
+  def read_unmapped?
+    @flag & $flags[3] != 0
+  end
+
+  def mate_unmapped?
+    @flag & $flags[4] != 0
+  end
+
+  def read_reverse_strand?
+    @flag & $flags[5] != 0
+  end
+
+  def mate_reverse_strand?
+    @flag & $flags[6] != 0
+  end
+
+  def first_in_pair?
+    @flag & $flags[7] != 0
+  end
+
+  def second_in_pair?
+    @flag & $flags[8] !=0
+  end
+
+  def primary_aln?
+    !(@flag & $flags[9]) != 0
+  end
+
+  def quality_fail?
+    @flag & $flags[10] != 0
+  end
+
+  def pcr_duplicate?
+    @flag & $flags[11] != 0
+  end
+
+  # pair convenience methods
+
+  def both_mapped?
+    !(self.read_unmapped? && self.mate_unmapped?)
+  end
+
+  def pair_opposite_strands?
+    (!self.read_reverse_strand? && self.mate_reverse_strand?) || 
+      (self.read_reverse_strand? && !self.mate_reverse_strand?)
+  end
+
+  def pair_same_strand?
+    !self.pair_opposite_strands?
+  end
+
+
+private
+
+  def int_or_neg1(x)
+    Integer(x) rescue -1
+  end
+
+  def int_or_raw(x)
+    Integer(x) rescue x
+  end
+
+end

metadata

@@ -0,0 +1,47 @@
+--- !ruby/object:Gem::Specification
+name: bettersam
+version: !ruby/object:Gem::Version
+  version: 0.0.1.alpha
+  prerelease: 6
+platform: ruby
+authors:
+- Richard Smith
+- Jesse Rodriguez
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-09-17 00:00:00.000000000 Z
+dependencies: []
+description: Extended SAM (Sequence Alignment/Map) file parsing
+email: rds45@cam.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/bettersam.rb
+homepage: https://github.com/blahah/bettersam
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Extended SAM file parsing
+test_files: []