-Added the IDs to test

-Capacity to calculate the average coverage of certain region without unnecesary allocation.

Rakefile

@@ -1,10 +1,11 @@
-require 'echoe'
+#require 'echoe'
 
-Echoe.new("samtools-ruby", version=0.1) do |p|
-   p.author = "Ricardo H. Ramirez-Gonzalez"
-   p.summary = "Binder of samtools for ruby, on the top of FFI. "
-   p.url = "http://github.com/homonecloco/samtools-ruby"
-end
+#Echoe.new("samtools-ruby", version=0.1) do |p|
+#   p.author = "Ricardo H. Ramirez-Gonzalez"
+#   p.summary = "Binder of samtools for ruby, on the top of FFI. "
+#   p.url = "http://github.com/homonecloco/samtools-ruby"
+ #  p.platform = Gem
+#end
 
 
 desc "Basic test"

lib/bio/db/sam.rb

@@ -102,12 +102,38 @@ def load_reference()
 
       end
 
+      def average_coverage(chromosome, qstart, len)
+        reference = fetch_reference(chromosome, qstart, qstart+len)
+        len = reference.length if len > reference.length
+        #p qend.to_s + "-" + qstart.to_s + "framesize " + (qend - qstart).to_s
+        coverages = Array.new(len, 0)
+
+        avg_proc = Proc.new do |alignment|
+          last = qstart + len
+          first = qstart
+          last = alignment.calend if last > alignment.calend
+          first = alignment.pos if first < alignment.pos
+          p first
+          first.upto(last-1) { |i|
+             coverages[first-i] = 1 + coverages[first-i] }
+        end
+
+        fetch_with_function(chromosome, qstart, qstart+len, avg_proc)
+        p coverages
+        total = 0
+        0.upto(len-1) { |i| total= total + coverages[i] }
+        avg_cov = total.to_f / len
+        #LibC.free referemce
+        avg_cov
+      end
+
       def fetch_reference(chromosome, qstart,qend)
-        load_reference unless @fasta_index.nil? || @fasta_index.null? 
+        load_reference if @fasta_index.nil? || @fasta_index.null? 
         query = query_string(chromosome, qstart,qend)
         len = FFI::MemoryPointer.new :int
         reference = Bio::DB::SAM::Tools.fai_fetch(@fasta_index, query, len)
         raise SAMException.new(), "Unable to get sequence for reference: "+query if reference.nil?
+
         reference
       end
 

test/basictest.rb

@@ -87,6 +87,30 @@ def test_class_binary_read_no_close
     assert(true, "BINARY file openend but not closed")  
   end
 
+  def test_read_coverage
+     sam       = Bio::DB::Sam.new({:bam=>@testBAMFile, :fasta=>@testReference})
+     sam.open
+  	File.open( @test_folder +"/ids2.txt", "r") do |file|
+  	  puts "file opened"
+  	  file.each_line{|line|
+        fetching = line.split(' ')[0]
+        puts "fetching: " + fetching
+  	    sam.load_reference
+    	  seq = sam.fetch_reference(fetching, 0, 16000)
+  #	  puts seq 
+  #	  puts seq.length
+  	  als = sam.fetch(fetching, 0, seq.length) 
+     #      p als
+  	  if als.length() > 0 then
+  	       p fetching
+                p als
+  	    end
+           }
+
+  	end
+    sam.close
+   assert(true, "Finish")
+  end
 #  def test_read_TAM_as_BAM
 #    begin
 #      sam                          = Bio::DB::Sam.new({:bam=>@testTAMFile})
@@ -228,6 +252,17 @@ def test_load_feature
     p fs
     assert(true, "Loaded as features")
   end
+
+  def test_avg_coverage
+    sam = Bio::DB::Sam.new({:fasta=>@testReference, :bam=>@testBAMFile })
+    sam.open
+    cov = sam.average_coverage("chr_1", 60, 30)
+    p "Coverage: " + cov.to_s
+    sam.close
+    assert(true, "Average coverage ran")
+    assert(3 == cov, "The coverage is 3")
+  end
+
 
 end
 

test/samples/small/ids2.txt

@@ -0,0 +1 @@
+chr_1