bio-ucsc-util 0.1.0 → 0.1.1
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- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/bio-ucsc-util.gemspec +3 -3
- data/ext/ucsc-util/README +26 -14
- data/ext/ucsc-util/ucsc-util-src-v268.tgz +0 -0
- data/lib/bio/ucsc/big_wig.rb +9 -1
- data/lib/bio/ucsc/binding.rb +1 -1
- metadata +5 -5
data/Rakefile
CHANGED
@@ -18,7 +18,7 @@ Jeweler::Tasks.new do |gem|
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gem.homepage = "http://github.com/throwern/bio-ucsc-util"
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gem.license = "MIT"
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gem.summary = %Q{Ruby binding to the ucsc kent utilities}
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21
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-
gem.description = %Q{Ruby FFI binding
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21
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+
gem.description = %Q{Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig}
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gem.email = "throwern@msu.edu"
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gem.authors = ["throwern"]
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# dependencies defined in Gemfile
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.1
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data/bio-ucsc-util.gemspec
CHANGED
@@ -5,12 +5,12 @@
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5
5
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6
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Gem::Specification.new do |s|
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s.name = "bio-ucsc-util"
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8
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-
s.version = "0.1.
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8
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+
s.version = "0.1.1"
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9
9
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["throwern"]
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12
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-
s.date = "2012-
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-
s.description = "Ruby FFI binding
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12
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+
s.date = "2012-10-02"
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13
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+
s.description = "Ruby FFI binding of the ucsc kent src. Implemented utilities include: bigWigInfo, bigWigSummary and wigToBigWig"
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s.email = "throwern@msu.edu"
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s.extensions = ["ext/ucsc-util/mkrf_conf.rb"]
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s.extra_rdoc_files = [
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data/ext/ucsc-util/README
CHANGED
@@ -5,20 +5,32 @@ These folders have been extracted into an archive for use by this rubygem.
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5
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The data was retrieved from:
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http://hgdownload.cse.ucsc.edu/admin/jksrc.v268.zip
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-
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-
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-
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11
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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8
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+
Some modifications of the code may be required for this rubygem to operate:
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9
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+
1.)
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10
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+
Some original source files have additional functions defined that rely on static (private) methods. New versions
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11
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+
need to incorporate these changes. They are required in order to build the additional bigWigSmooth utility.
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12
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+
bigWigFileSmooth
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+
bwgSmoothAvg
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+
bwgSmoothProbe
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+
testInterval
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+
setupVariableBigWig
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+
Files Altered:
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+
inc/bwgInternal.h
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+
inc/bigWig.h
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+
lib/bwgCreate.c
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+
Additional Utility:
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+
utils/bigWigSmooth/bigWigSmooth.c
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2.)
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+
cheapcgi.h/c has a conditional **environ definition to support shared libraries on OSX
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+
#ifndef __APPLE__
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extern char **environ;
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INLINE char **getEnviron() {return environ;}
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#else
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#include <crt_externs.h>
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INLINE char **getEnviron() { return (*_NSGetEnviron()); }
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#endif
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3.)
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added line: 1086 - lineFileClose(&lf); bwgParseBigWig() in bwgCreate.c. Method was leaking open file descriptors
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34
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---Original README below
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36
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Binary file
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data/lib/bio/ucsc/big_wig.rb
CHANGED
@@ -37,7 +37,15 @@ module Bio
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end
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# closes the file
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def close
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-
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+
puts "@bbi_file=#{bbi_file}"
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bound_bbi = Binding::BbiFile.new(bbi_file)
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puts "Binding::BbiFile=#{bound_bbi}"
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puts "Binding::to_ptr=#{bound_bbi.to_ptr}"
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if bbi_file
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bbi_ptr= FFI::MemoryPointer.new(:pointer)
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bbi_ptr.write_pointer(bbi_file)
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Binding::bbiFileClose(bbi_ptr)
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end
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@bbi_file = nil
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end
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# returns the caclulated standard deviation
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data/lib/bio/ucsc/binding.rb
CHANGED
@@ -106,7 +106,7 @@ module Bio
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# bbi
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attach_function :bbiChromList, [:pointer], :pointer # *bbiFile ; BbiChromInfo*
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attach_function :bbiChromSize, [:pointer,:pointer], :int32 # *bbiFile, chrom ; size
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-
attach_function :bbiFileClose, [:pointer], :void #
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+
attach_function :bbiFileClose, [:pointer], :void # **bbiFile
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attach_function :bbiTotalSummary, [:pointer], BbiSummaryElement.by_value # **bbiFile
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attach_function :bbiSummaryTypeFromString, [:string], BbiSummaryType # summaryType
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# bigwig
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bio-ucsc-util
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version: !ruby/object:Gem::Version
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-
version: 0.1.
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+
version: 0.1.1
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-
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+
date: 2012-10-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: ffi
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@@ -75,8 +75,8 @@ dependencies:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.8.3
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-
description: ! 'Ruby FFI binding
|
79
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-
bigWigSummary and wigToBigWig'
|
78
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+
description: ! 'Ruby FFI binding of the ucsc kent src. Implemented utilities include:
|
79
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+
bigWigInfo, bigWigSummary and wigToBigWig'
|
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email: throwern@msu.edu
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executables: []
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extensions:
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@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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version: '0'
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segments:
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- 0
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-
hash:
|
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+
hash: 3159547911850259478
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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