bio-ucsc-util 0.1.0 → 0.1.1

data/Rakefile

@@ -18,7 +18,7 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/throwern/bio-ucsc-util"
   gem.license = "MIT"
   gem.summary = %Q{Ruby binding to the ucsc kent utilities}
-  gem.description = %Q{Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo, bigWigSummary and wigToBigWig}
+  gem.description = %Q{Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig}
   gem.email = "throwern@msu.edu"
   gem.authors = ["throwern"]
   # dependencies defined in Gemfile

data/VERSION

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

data/bio-ucsc-util.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-util"
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["throwern"]
-  s.date = "2012-08-07"
-  s.description = "Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo, bigWigSummary and wigToBigWig"
+  s.date = "2012-10-02"
+  s.description = "Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig"
   s.email = "throwern@msu.edu"
   s.extensions = ["ext/ucsc-util/mkrf_conf.rb"]
   s.extra_rdoc_files = [

data/ext/ucsc-util/README

@@ -5,20 +5,32 @@ These folders have been extracted into an archive for use by this rubygem.
 The data was retrieved from:
 http://hgdownload.cse.ucsc.edu/admin/jksrc.v268.zip
 
-3 of the original source files have modified code that relies on static (private) methods. New versions need to incorporate these changes.
-See bigWigSmooth in:
--inc/bwgInternal.h
--inc/bigWig.h
--lib/bwgCreate.c
-
-Also converted **environ calls to support OSX shared library in cheapcgi.h/c
-#if defined __environ
-    extern char **environ;
-    INLINE char **getEnviron() {return environ;}
-#else
-    #include <crt_externs.h>
-    INLINE char **getEnviron() { return (*_NSGetEnviron()); }
-#endif
+Some modifications of the code may be required for this rubygem to operate:
+1.)
+	Some original source files have additional functions defined that rely on static (private) methods. New versions 
+	need to incorporate these changes. They are required in order to build the additional bigWigSmooth utility.
+		bigWigFileSmooth
+		bwgSmoothAvg
+		bwgSmoothProbe
+		testInterval
+		setupVariableBigWig
+	Files Altered:
+		inc/bwgInternal.h
+		inc/bigWig.h
+		lib/bwgCreate.c
+	Additional Utility:
+		utils/bigWigSmooth/bigWigSmooth.c
+2.)	
+	cheapcgi.h/c has a conditional **environ definition to support shared libraries on OSX
+		#ifndef __APPLE__
+		    extern char **environ;
+		    INLINE char **getEnviron() {return environ;}
+		#else
+		    #include <crt_externs.h>
+		    INLINE char **getEnviron() { return (*_NSGetEnviron()); }
+		#endif
+3.)
+	added line: 1086 - lineFileClose(&lf); bwgParseBigWig() in bwgCreate.c. Method was leaking open file descriptors
 
 ---Original README below
 

data/lib/bio/ucsc/big_wig.rb

@@ -37,7 +37,15 @@ module Bio
       end
       # closes the file
       def close
-        Binding::bbiFileClose(bbi_file) if bbi_file
+        puts "@bbi_file=#{bbi_file}"
+        bound_bbi = Binding::BbiFile.new(bbi_file)
+        puts "Binding::BbiFile=#{bound_bbi}"
+        puts "Binding::to_ptr=#{bound_bbi.to_ptr}"
+        if bbi_file
+          bbi_ptr= FFI::MemoryPointer.new(:pointer)
+          bbi_ptr.write_pointer(bbi_file)
+          Binding::bbiFileClose(bbi_ptr)
+        end
         @bbi_file = nil
       end
       # returns the caclulated standard deviation

data/lib/bio/ucsc/binding.rb

@@ -106,7 +106,7 @@ module Bio
       # bbi
       attach_function :bbiChromList, [:pointer], :pointer                                                     # *bbiFile ; BbiChromInfo*
       attach_function :bbiChromSize, [:pointer,:pointer], :int32                                              # *bbiFile, chrom ; size
-      attach_function :bbiFileClose, [:pointer], :void                                                        # *bbiFile
+      attach_function :bbiFileClose, [:pointer], :void                                                        # **bbiFile
       attach_function :bbiTotalSummary, [:pointer], BbiSummaryElement.by_value                                # **bbiFile
       attach_function :bbiSummaryTypeFromString, [:string], BbiSummaryType                                    # summaryType
       # bigwig

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-util
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-07 00:00:00.000000000 Z
+date: 2012-10-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -75,8 +75,8 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.8.3
-description: ! 'Ruby FFI binding and implmentation of the ucsc utilities: bigWigInfo,
-  bigWigSummary and wigToBigWig'
+description: ! 'Ruby FFI binding of the ucsc kent src. Implemented utilities include:
+  bigWigInfo, bigWigSummary and wigToBigWig'
 email: throwern@msu.edu
 executables: []
 extensions:
@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1186691304766418588
+      hash: 3159547911850259478
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: