sam 0.0.1

data/lib/sam.rb

@@ -0,0 +1,53 @@
+class Sam
+public
+  attr_accessor :name, :flag, :chrom, :pos, :mapq, :cigar, :mchrom, :mpos, :insert, :seq, :qual, :tags
+
+  def initialize(line=nil)
+    @tags = {}
+    parse_line(line) if line != nil
+  end
+
+  def int_or_neg1(x)
+    Integer(x) rescue -1
+  end
+
+  def int_or_raw(x)
+    Integer(x) rescue x
+  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 = 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
+
+end

metadata

@@ -0,0 +1,54 @@
+--- !ruby/object:Gem::Specification 
+name: sam
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Jesse Rodriguez
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-07-06 00:00:00 Z
+dependencies: []
+
+description: Lightweight SAM (Sequence Alignment/Map) file parsing
+email: jesserod@cs.stanford.edu
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- lib/sam.rb
+homepage: http://rubygems.org/gems/sam
+licenses: []
+
+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: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.8.5
+signing_key: 
+specification_version: 3
+summary: Lightweight SAM file parsing
+test_files: []
+