bio-bgzf 0.1.0 → 0.1.1

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/lib/bio-bgzf/block.rb

@@ -36,14 +36,14 @@ module Bio::BGZF
   def decompress_block(f)
     cdata, in_size, expected_crc = read_bgzf_block(f)
     return nil if cdata == nil
-    crc = Zlib.crc32(cdata, 0)
-    if crc != expected_crc
-      raise "CRC error: expected #{expected_crc.to_s(16)}, got #{crc.to_s(16)}"
-    end
     data = unpack(cdata)
     if data.bytesize != in_size
       raise "Expected #{in_size} bytes from BGZF block at #{pos}, but got #{data.bytesize} bytes!"
     end
+    crc = Zlib.crc32(data, 0)
+    if crc != expected_crc
+      raise "CRC error: expected #{expected_crc.to_s(16)}, got #{crc.to_s(16)}"
+    end
     return data
   end
   module_function :decompress_block

data/lib/bio-bgzf/pack.rb

@@ -9,7 +9,7 @@ module Bio::BGZF
     cdata = zs.deflate str, Zlib::FINISH
     zs.close
 
-    crc32 = Zlib.crc32 cdata, 0
+    crc32 = Zlib.crc32 str, 0
     isize = str.length
 
     bsize = cdata.length + 19 + XLEN

data/spec/bio-bgzf_spec.rb

@@ -8,6 +8,15 @@ describe Bio::BGZF do
     Bio::BGZF.pack("asdfghjkl").should be_instance_of String
   end
 
+  it "should be able to read BGZF blocks from a samtools file" do
+    File.open("test/data/mm8.chrM.maf.gz") do |f|
+      r = Bio::BGZF::Reader.new(f)
+      r.each_block do |block|
+        block.size.should <= 65536
+      end
+    end
+  end
+
   it "should be able to iteratively read BGZF blocks from stream" do
     str = ''
     1000.times { str += (Random.rand(26) + 65).chr }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-bgzf
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -89,6 +89,7 @@ files:
 - lib/bio-bgzf/unpack.rb
 - lib/bio-bgzf/vo.rb
 - spec/bio-bgzf_spec.rb
+- test/data/mm8.chrM.maf.gz
 homepage: http://github.com/csw/bioruby-bgzf
 licenses:
 - MIT
@@ -104,7 +105,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2167366817840907754
+      hash: 887449106420092676
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: