bio-bgzf 0.2.0 → 0.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/VERSION +1 -1
- data/lib/bio-bgzf/writer.rb +19 -3
- metadata +3 -3
data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.2.
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1
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+
0.2.1
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data/lib/bio-bgzf/writer.rb
CHANGED
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@@ -1,13 +1,21 @@
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1
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+
require 'zlib'
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2
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+
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module Bio::BGZF
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4
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class Writer
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include Bio::BGZF
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7
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6
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-
attr_reader :f, :buf
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8
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+
attr_reader :f, :buf, :level
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9
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+
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10
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# Return the virtual offset of the last {#write} call. This is a
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11
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# hook for e.g. building an index on the fly.
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12
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attr_reader :last_write_pos
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13
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8
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-
def initialize(f)
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14
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def initialize(f, level=2)
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@f = f
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@level = level
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10
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@buf = ''
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@buf_write_pos = 0
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if block_given?
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begin
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yield self
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@@ -24,15 +32,22 @@ module Bio::BGZF
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def write_buf
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if buf.size > 0
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raise "Buffer too large: #{buf.bytesize}" if buf.bytesize > MAX_BYTES
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-
block = pack(buf)
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35
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block = pack(buf, level)
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f.write(block)
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@buf = ''
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38
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@buf_write_pos = tell
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end
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end
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42
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# @api private
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43
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def _cur_write_pos
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@buf_write_pos + buf.bytesize
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end
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46
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+
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def write(s)
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if s.bytesize > MAX_BYTES
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write_buf
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@last_write_pos = _cur_write_pos
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_each_slice(s) do |slice|
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write(slice)
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end
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@@ -40,6 +55,7 @@ module Bio::BGZF
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if (s.bytesize + buf.bytesize) > MAX_BYTES
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write_buf
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end
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@last_write_pos = _cur_write_pos
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buf << s
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end
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bio-bgzf
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version: !ruby/object:Gem::Version
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-
version: 0.2.
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version: 0.2.1
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prerelease:
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platform: ruby
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authors:
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@@ -10,7 +10,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-08-
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date: 2012-08-06 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -104,7 +104,7 @@ 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: -2944900178146430147
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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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