vcf 0.0.1 → 0.0.2

data/lib/vcf.rb

@@ -2,59 +2,59 @@ class Vcf
 public
   attr_accessor :chrom, :pos, :id, :ref, :alt, :qual, :filter, :info, :format, :samples
 
-  def initialize(line=nil)
-    samples = {}
+  def initialize(line=nil, sample_names=nil)
+    @info = {}
+    @samples = {}
+    parse_line(line, sample_names) if line != nil
   end
 
   def parse_line(line, sample_names=nil)
-    f = line.split("\t", -1)
+    f = line.chomp.split("\t", -1)
     raise "VCF lines must have at least 8 fields" if f.size < 8
-    chrom = f[0]
-    pos = f[1].to_i
-    id = f[2]
-    ref = f[3]
-    alt = f[4]
-    qual = f[5].to_i
-    filter = f[6]
-
-    info = {}
+    @chrom = f[0]
+    @pos = f[1].to_i
+    @id = f[2]
+    @ref = f[3]
+    @alt = f[4]
+    @qual = f[5].to_i
+    @filter = f[6]
+
+    @info = {}
     info_vec = f[7].split(";")
     info_vec.each do |x|
       keyval = x.split("=", -1)
       if keyval.size == 2 # If it's key=value
-        info[keyval[0]] = keyval[1]
+        @info[keyval[0]] = keyval[1]
       else # Otherwise, it's just a flag
-        info[x] = ""
+        @info[x] = ""
       end
     end
 
-    samples = {}
+    @samples = {}
     return true if f.size == 8  # Has just upto info
     raise "Can't have format with no samples" if f.size == 9
     
-    format = f[8]
+    @format = f[8]
 
-    sample_keys = format.split(":")
+    sample_keys = @format.split(":")
 
     num_samples = f.size - 9 # How many fields are past the format
 
     if sample_names == nil # Make the sample names just ["1", "2", ... , "num_samples}"
       sample_names = (1..num_samples).to_a.map{|i| i.to_s} 
-    elsif f.size != num_samples
-      raise "Expected #{sample_names.size} but got #{num_samples}"
+    elsif sample_names.size != num_samples
+      raise "Unexpected number of samples (#{num_samples}) based on the provided sample names (#{sample_names.inspect})"
     end
 
     sample_names.each_with_index do |sample_name, sample_index|
       i = sample_index + 9 # index into columns (f)
       sample_values = f[i].split(":")
-      raise "Expected number of sample values to match number of sample keys in FORMAT column" if sample_values.size != sample_keys.size
-      samples[sample_name] = {}
-      sample_keys.each_with_index {|key, value_index| samples[sample_name][k] = sample_values[value_index]}
+      raise "Expected number of sample values to be <= number of sample keys in FORMAT column Format=#{@format} but sample=#{f[i]}" if sample_values.size > sample_keys.size
+      @samples[sample_name] = {}
+      sample_keys.each_with_index {|key, value_index| @samples[sample_name][key] = sample_values[value_index] || ""}
     end
     
     return true;
   end
 
-private
-  attr_accessor :
 end

metadata

@@ -2,7 +2,7 @@
 name: vcf
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors: 
 - Jesse Rodriguez