RubyGems - bio-samtools-wrapper - Versions diffs - 2.7.0 - Mend

bio-samtools-wrapper 2.7.0

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checksums.yaml +7 -0
data/.document +5 -0
data/.travis.yml +27 -0
data/Gemfile +20 -0
data/LICENSE.txt +702 -0
data/README.md +501 -0
data/Rakefile +73 -0
data/VERSION +1 -0
data/bin/bam_consensus.rb +85 -0
data/bio-samtools-wrapper.gemspec +181 -0
data/doc/Bio/DB/Alignment.html +552 -0
data/doc/Bio/DB/Pileup.html +711 -0
data/doc/Bio/DB/SAM/Library.html +167 -0
data/doc/Bio/DB/SAM/Tools.html +109 -0
data/doc/Bio/DB/SAM.html +1853 -0
data/doc/Bio/DB/Tag.html +208 -0
data/doc/Bio/DB/Vcf.html +431 -0
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data/doc/table_of_contents.html +305 -0
data/ext/Makefile-bioruby.patch +12 -0
data/ext/Makefile-suse.patch +11 -0
data/ext/mkrf_conf.rb +118 -0
data/lib/bio/BIOExtensions.rb +89 -0
data/lib/bio/db/alignment.rb +64 -0
data/lib/bio/db/fastadb.rb +320 -0
data/lib/bio/db/pileup.rb +273 -0
data/lib/bio/db/sam/external/COPYING +21 -0
data/lib/bio/db/sam/external/VERSION +1 -0
data/lib/bio/db/sam/library.rb +32 -0
data/lib/bio/db/sam.rb +778 -0
data/lib/bio/db/vcf.rb +105 -0
data/lib/bio-samtools-wrapper.rb +9 -0
data/test/.gitignore +1 -0
data/test/helper.rb +18 -0
data/test/sample.vcf +24 -0
data/test/samples/.gitignore +1 -0
data/test/samples/LCI/NC_001988.ffn +2 -0
data/test/samples/LCI/test.bam +0 -0
data/test/samples/LCI/test.bam.bai +0 -0
data/test/samples/small/dupes.bam +0 -0
data/test/samples/small/dupes.sam +274 -0
data/test/samples/small/ids2.txt +1 -0
data/test/samples/small/map_for_reheader.sam +8 -0
data/test/samples/small/map_to_merge1.bam +0 -0
data/test/samples/small/map_to_merge1.bam.bai +0 -0
data/test/samples/small/map_to_merge1.sam +8 -0
data/test/samples/small/map_to_merge2.bam +0 -0
data/test/samples/small/map_to_merge2.bam.bai +0 -0
data/test/samples/small/map_to_merge2.sam +8 -0
data/test/samples/small/no_md.sam +8 -0
data/test/samples/small/sorted.bam +0 -0
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data/test/samples/small/test.sai +0 -0
data/test/samples/small/test.tam +10 -0
data/test/samples/small/test_chr.fasta +1000 -0
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data/test/samples/small/test_chr.fasta.amb +2 -0
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data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rpac +0 -0
data/test/samples/small/test_chr.fasta.rsa +0 -0
data/test/samples/small/test_chr.fasta.sa +0 -0
data/test/samples/small/test_cov.svg +273 -0
data/test/samples/small/test_fastadb.fasta +34 -0
data/test/samples/small/testu.bam +0 -0
data/test/samples/small/testu.bed +2 -0
data/test/test_bio-samtools-wrapper.rb +1 -0
data/test/test_fastadb.rb +89 -0
data/test/test_pileup.rb +90 -0
data/test/test_sam.rb +421 -0
data/test/test_vcf.rb +79 -0
data/tutorial/tutorial.html +474 -0
data/tutorial/tutorial.md +424 -0
data/tutorial/tutorial.pdf +0 -0
metadata +254 -0

data/doc/LICENSE_txt.html ADDED Viewed

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+<pre class="ruby">  <span class="ruby-identifier">a</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">in</span>, <span class="ruby-keyword">or</span> <span class="ruby-identifier">embodied</span> <span class="ruby-keyword">in</span>, <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">product</span>
+  (<span class="ruby-identifier">including</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">distribution</span> <span class="ruby-identifier">medium</span>), <span class="ruby-identifier">accompanied</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">fixed</span> <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">durable</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">medium</span>
+  <span class="ruby-identifier">customarily</span> <span class="ruby-identifier">used</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">software</span> <span class="ruby-identifier">interchange</span>.
+  <span class="ruby-identifier">b</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">in</span>, <span class="ruby-keyword">or</span> <span class="ruby-identifier">embodied</span> <span class="ruby-keyword">in</span>, <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">product</span>
+  (<span class="ruby-identifier">including</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">physical</span> <span class="ruby-identifier">distribution</span> <span class="ruby-identifier">medium</span>), <span class="ruby-identifier">accompanied</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">a</span>
+  <span class="ruby-identifier">written</span> <span class="ruby-identifier">offer</span>, <span class="ruby-identifier">valid</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">least</span> <span class="ruby-identifier">three</span> <span class="ruby-identifier">years</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">valid</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">as</span>
+  <span class="ruby-identifier">long</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">spare</span> <span class="ruby-identifier">parts</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">customer</span> <span class="ruby-identifier">support</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">product</span>
+  <span class="ruby-identifier">model</span>, <span class="ruby-identifier">to</span> <span class="ruby-identifier">give</span> <span class="ruby-identifier">anyone</span> <span class="ruby-identifier">who</span> <span class="ruby-identifier">possesses</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">either</span> (<span class="ruby-value">1</span>) <span class="ruby-identifier">a</span>
+  <span class="ruby-identifier">copy</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">all</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">software</span> <span class="ruby-keyword">in</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-identifier">product</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">covered</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">this</span> <span class="ruby-constant">License</span>, <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">durable</span> <span class="ruby-identifier">physical</span>
+  <span class="ruby-identifier">medium</span> <span class="ruby-identifier">customarily</span> <span class="ruby-identifier">used</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">software</span> <span class="ruby-identifier">interchange</span>, <span class="ruby-keyword">for</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">price</span> <span class="ruby-identifier">no</span>
+  <span class="ruby-identifier">more</span> <span class="ruby-identifier">than</span> <span class="ruby-identifier">your</span> <span class="ruby-identifier">reasonable</span> <span class="ruby-identifier">cost</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">physically</span> <span class="ruby-identifier">performing</span> <span class="ruby-identifier">this</span>
+  <span class="ruby-identifier">conveying</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">source</span>, <span class="ruby-keyword">or</span> (<span class="ruby-value">2</span>) <span class="ruby-identifier">access</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">from</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">network</span> <span class="ruby-identifier">server</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span> <span class="ruby-identifier">charge</span>.
+  <span class="ruby-identifier">c</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">individual</span> <span class="ruby-identifier">copies</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-identifier">written</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">provide</span> <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>.  <span class="ruby-constant">This</span>
+  <span class="ruby-identifier">alternative</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">allowed</span> <span class="ruby-identifier">only</span> <span class="ruby-identifier">occasionally</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">noncommercially</span>, <span class="ruby-keyword">and</span>
+  <span class="ruby-identifier">only</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">received</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">such</span> <span class="ruby-identifier">an</span> <span class="ruby-identifier">offer</span>, <span class="ruby-keyword">in</span> <span class="ruby-identifier">accord</span>
+  <span class="ruby-identifier">with</span> <span class="ruby-identifier">subsection</span> <span class="ruby-value">6</span><span class="ruby-identifier">b</span>.
+  <span class="ruby-identifier">d</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">offering</span> <span class="ruby-identifier">access</span> <span class="ruby-identifier">from</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">designated</span>
+  <span class="ruby-identifier">place</span> (<span class="ruby-identifier">gratis</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">charge</span>), <span class="ruby-keyword">and</span> <span class="ruby-identifier">offer</span> <span class="ruby-identifier">equivalent</span> <span class="ruby-identifier">access</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-keyword">in</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">same</span> <span class="ruby-identifier">way</span> <span class="ruby-identifier">through</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">same</span> <span class="ruby-identifier">place</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span>
+  <span class="ruby-identifier">further</span> <span class="ruby-identifier">charge</span>.  <span class="ruby-constant">You</span> <span class="ruby-identifier">need</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">require</span> <span class="ruby-identifier">recipients</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span> <span class="ruby-identifier">along</span> <span class="ruby-identifier">with</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span>.  <span class="ruby-constant">If</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">place</span> <span class="ruby-identifier">to</span>
+  <span class="ruby-identifier">copy</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">network</span> <span class="ruby-identifier">server</span>, <span class="ruby-identifier">the</span> <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>
+  <span class="ruby-identifier">may</span> <span class="ruby-identifier">be</span> <span class="ruby-identifier">on</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">different</span> <span class="ruby-identifier">server</span> (<span class="ruby-identifier">operated</span> <span class="ruby-identifier">by</span> <span class="ruby-identifier">you</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">a</span> <span class="ruby-identifier">third</span> <span class="ruby-identifier">party</span>)
+  <span class="ruby-identifier">that</span> <span class="ruby-identifier">supports</span> <span class="ruby-identifier">equivalent</span> <span class="ruby-identifier">copying</span> <span class="ruby-identifier">facilities</span>, <span class="ruby-identifier">provided</span> <span class="ruby-identifier">you</span> <span class="ruby-identifier">maintain</span>
+  <span class="ruby-identifier">clear</span> <span class="ruby-identifier">directions</span> <span class="ruby-keyword">next</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">saying</span> <span class="ruby-identifier">where</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">find</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>.  <span class="ruby-constant">Regardless</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">what</span> <span class="ruby-identifier">server</span> <span class="ruby-identifier">hosts</span> <span class="ruby-identifier">the</span>
+  <span class="ruby-constant">Corresponding</span> <span class="ruby-constant">Source</span>, <span class="ruby-identifier">you</span> <span class="ruby-identifier">remain</span> <span class="ruby-identifier">obligated</span> <span class="ruby-identifier">to</span> <span class="ruby-keyword">ensure</span> <span class="ruby-identifier">that</span> <span class="ruby-identifier">it</span> <span class="ruby-identifier">is</span>
+  <span class="ruby-identifier">available</span> <span class="ruby-keyword">for</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">long</span> <span class="ruby-identifier">as</span> <span class="ruby-identifier">needed</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">satisfy</span> <span class="ruby-identifier">these</span> <span class="ruby-identifier">requirements</span>.
+  <span class="ruby-identifier">e</span>) <span class="ruby-constant">Convey</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">using</span> <span class="ruby-identifier">peer</span><span class="ruby-operator">-</span><span class="ruby-identifier">to</span><span class="ruby-operator">-</span><span class="ruby-identifier">peer</span> <span class="ruby-identifier">transmission</span>, <span class="ruby-identifier">provided</span>
+  <span class="ruby-identifier">you</span> <span class="ruby-identifier">inform</span> <span class="ruby-identifier">other</span> <span class="ruby-identifier">peers</span> <span class="ruby-identifier">where</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span> <span class="ruby-keyword">and</span> <span class="ruby-constant">Corresponding</span>
+  <span class="ruby-constant">Source</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">work</span> <span class="ruby-identifier">are</span> <span class="ruby-identifier">being</span> <span class="ruby-identifier">offered</span> <span class="ruby-identifier">to</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">general</span> <span class="ruby-identifier">public</span> <span class="ruby-identifier">at</span> <span class="ruby-identifier">no</span>
+  <span class="ruby-identifier">charge</span> <span class="ruby-identifier">under</span> <span class="ruby-identifier">subsection</span> <span class="ruby-value">6</span><span class="ruby-identifier">d</span>.
+<span class="ruby-constant">A</span> <span class="ruby-identifier">separable</span> <span class="ruby-identifier">portion</span> <span class="ruby-identifier">of</span> <span class="ruby-identifier">the</span> <span class="ruby-identifier">object</span> <span class="ruby-identifier">code</span>, <span class="ruby-identifier">whose</span> <span class="ruby-identifier">source</span> <span class="ruby-identifier">code</span> <span class="ruby-identifier">is</span> <span class="ruby-identifier">excluded</span>
+</pre>
+<p>from the Corresponding Source as a System Library, need not be included in
+conveying the object code work.</p>
+<pre>A &quot;User Product&quot; is either (1) a &quot;consumer product&quot;, which means any</pre>
+<p>tangible personal property which is normally used for personal, family, or
+household purposes, or (2) anything designed or sold for incorporation into
+a dwelling.  In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage.  For a particular
+product received by a particular user, “normally used” refers to a typical
+or common use of that class of product, regardless of the status of the
+particular user or of the way in which the particular user actually uses,
+or expects or is expected to use, the product.  A product is a consumer
+product regardless of whether the product has substantial commercial,
+industrial or non-consumer uses, unless such uses represent the only
+significant mode of use of the product.</p>
+<pre>&quot;Installation Information&quot; for a User Product means any methods,</pre>
+<p>procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from a
+modified version of its Corresponding Source.  The information must suffice
+to ensure that the continued functioning of the modified object code is in
+no case prevented or interfered with solely because modification has been
+made.</p>
+<pre>If you convey an object code work under this section in, or with, or</pre>
+<p>specifically for use in, a User Product, and the conveying occurs as part
+of a transaction in which the right of possession and use of the User
+Product is transferred to the recipient in perpetuity or for a fixed term
+(regardless of how the transaction is characterized), the Corresponding
+Source conveyed under this section must be accompanied by the Installation
+Information.  But this requirement does not apply if neither you nor any
+third party retains the ability to install modified object code on the User
+Product (for example, the work has been installed in ROM).</p>
+<pre>The requirement to provide Installation Information does not include a</pre>
+<p>requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for the
+User Product in which it has been modified or installed.  Access to a
+network may be denied when the modification itself materially and adversely
+affects the operation of the network or violates the rules and protocols
+for communication across the network.</p>
+<pre>Corresponding Source conveyed, and Installation Information provided,</pre>
+<p>in accord with this section must be in a format that is publicly documented
+(and with an implementation available to the public in source code form),
+and must require no special password or key for unpacking, reading or
+copying.</p>
+<pre>7. Additional Terms.
+&quot;Additional permissions&quot; are terms that supplement the terms of this</pre>
+<p>License by making exceptions from one or more of its conditions. Additional
+permissions that are applicable to the entire Program shall be treated as
+though they were included in this License, to the extent that they are
+valid under applicable law.  If additional permissions apply only to part
+of the Program, that part may be used separately under those permissions,
+but the entire Program remains governed by this License without regard to
+the additional permissions.</p>
+<pre>When you convey a copy of a covered work, you may at your option</pre>
+<p>remove any additional permissions from that copy, or from any part of it.
+(Additional permissions may be written to require their own removal in
+certain cases when you modify the work.)  You may place additional
+permissions on material, added by you to a covered work, for which you have
+or can give appropriate copyright permission.</p>
+<pre>Notwithstanding any other provision of this License, for material you</pre>
+<p>add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:</p>
+<pre>  a) Disclaiming warranty or limiting liability differently from the
+  terms of sections 15 and 16 of this License; or
+  b) Requiring preservation of specified reasonable legal notices or
+  author attributions in that material or in the Appropriate Legal
+  Notices displayed by works containing it; or
+  c) Prohibiting misrepresentation of the origin of that material, or
+  requiring that modified versions of such material be marked in
+  reasonable ways as different from the original version; or
+  d) Limiting the use for publicity purposes of names of licensors or
+  authors of the material; or
+  e) Declining to grant rights under trademark law for use of some
+  trade names, trademarks, or service marks; or
+  f) Requiring indemnification of licensors and authors of that
+  material by anyone who conveys the material (or modified versions of
+  it) with contractual assumptions of liability to the recipient, for
+  any liability that these contractual assumptions directly impose on
+  those licensors and authors.
+All other non-permissive additional terms are considered &quot;further</pre>
+<p>restrictions“ within the meaning of section 10.  If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further restriction,
+you may remove that term.  If a license document contains a further
+restriction but permits relicensing or conveying under this License, you
+may add to a covered work material governed by the terms of that license
+document, provided that the further restriction does not survive such
+relicensing or conveying.</p>
+<pre>If you add terms to a covered work in accord with this section, you</pre>
+<p>must place, in the relevant source files, a statement of the additional
+terms that apply to those files, or a notice indicating where to find the
+applicable terms.</p>
+<pre>Additional terms, permissive or non-permissive, may be stated in the</pre>
+<p>form of a separately written license, or stated as exceptions; the above
+requirements apply either way.</p>
+<pre>8. Termination.
+You may not propagate or modify a covered work except as expressly</pre>
+<p>provided under this License.  Any attempt otherwise to propagate or modify
+it is void, and will automatically terminate your rights under this License
+(including any patent licenses granted under the third paragraph of section
+11).</p>
+<pre>However, if you cease all violation of this License, then your</pre>
+<p>license from a particular copyright holder is reinstated (a) provisionally,
+unless and until the copyright holder explicitly and finally terminates
+your license, and (b) permanently, if the copyright holder fails to notify
+you of the violation by some reasonable means prior to 60 days after the
+cessation.</p>
+<pre>Moreover, your license from a particular copyright holder is</pre>
+<p>reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after your
+receipt of the notice.</p>
+<pre>Termination of your rights under this section does not terminate the</pre>
+<p>licenses of parties who have received copies or rights from you under this
+License.  If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.</p>
+<pre>9. Acceptance Not Required for Having Copies.
+You are not required to accept this License in order to receive or</pre>
+<p>run a copy of the Program.  Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission to
+receive a copy likewise does not require acceptance.  However, nothing
+other than this License grants you permission to propagate or modify any
+covered work.  These actions infringe copyright if you do not accept this
+License.  Therefore, by modifying or propagating a covered work, you
+indicate your acceptance of this License to do so.</p>
+<pre>10. Automatic Licensing of Downstream Recipients.
+Each time you convey a covered work, the recipient automatically</pre>
+<p>receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License.  You are not responsible for
+enforcing compliance by third parties with this License.</p>
+<pre>An &quot;entity transaction&quot; is a transaction transferring control of an</pre>
+<p>organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations.  If propagation of a covered work
+results from an entity transaction, each party to that transaction who
+receives a copy of the work also receives whatever licenses to the work the
+party&#39;s predecessor in interest had or could give under the previous
+paragraph, plus a right to possession of the Corresponding Source of the
+work from the predecessor in interest, if the predecessor has it or can get
+it with reasonable efforts.</p>
+<pre>You may not impose any further restrictions on the exercise of the</pre>
+<p>rights granted or affirmed under this License.  For example, you may not
+impose a license fee, royalty, or other charge for exercise of rights
+granted under this License, and you may not initiate litigation (including
+a cross-claim or counterclaim in a lawsuit) alleging that any patent claim
+is infringed by making, using, selling, offering for sale, or importing the
+Program or any portion of it.</p>
+<pre>11. Patents.
+A &quot;contributor&quot; is a copyright holder who authorizes use under this</pre>
+<p>License of the Program or a work on which the Program is based.  The work
+thus licensed is called the contributor&#39;s “contributor version”.</p>
+<pre>A contributor&#39;s &quot;essential patent claims&quot; are all patent claims</pre>
+<p>owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted by
+this License, of making, using, or selling its contributor version, but do
+not include claims that would be infringed only as a consequence of further
+modification of the contributor version.  For purposes of this definition,
+“control” includes the right to grant patent sublicenses in a manner
+consistent with the requirements of this License.</p>
+<pre>Each contributor grants you a non-exclusive, worldwide, royalty-free</pre>
+<p>patent license under the contributor&#39;s essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.</p>
+<pre>In the following three paragraphs, a &quot;patent license&quot; is any express</pre>
+<p>agreement or commitment, however denominated, not to enforce a patent (such
+as an express permission to practice a patent or covenant not to sue for
+patent infringement).  To “grant” such a patent license to a party means to
+make such an agreement or commitment not to enforce a patent against the
+party.</p>
+<pre>If you convey a covered work, knowingly relying on a patent license,</pre>
+<p>and the Corresponding Source of the work is not available for anyone to
+copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means, then
+you must either (1) cause the Corresponding Source to be so available, or
+(2) arrange to deprive yourself of the benefit of the patent license for
+this particular work, or (3) arrange, in a manner consistent with the
+requirements of this License, to extend the patent license to downstream
+recipients.  “Knowingly relying” means you have actual knowledge that, but
+for the patent license, your conveying the covered work in a country, or
+your recipient&#39;s use of the covered work in a country, would infringe
+one or more identifiable patents in that country that you have reason to
+believe are valid.</p>
+<pre>If, pursuant to or in connection with a single transaction or</pre>
+<p>arrangement, you convey, or propagate by procuring conveyance of, a covered
+work, and grant a patent license to some of the parties receiving the
+covered work authorizing them to use, propagate, modify or convey a
+specific copy of the covered work, then the patent license you grant is
+automatically extended to all recipients of the covered work and works
+based on it.</p>
+<pre>A patent license is &quot;discriminatory&quot; if it does not include within</pre>
+<p>the scope of its coverage, prohibits the exercise of, or is conditioned on
+the non-exercise of one or more of the rights that are specifically granted
+under this License.  You may not convey a covered work if you are a party
+to an arrangement with a third party that is in the business of
+distributing software, under which you make payment to the third party
+based on the extent of your activity of conveying the work, and under which
+the third party grants, to any of the parties who would receive the covered
+work from you, a discriminatory patent license (a) in connection with
+copies of the covered work conveyed by you (or copies made from those
+copies), or (b) primarily for and in connection with specific products or
+compilations that contain the covered work, unless you entered into that
+arrangement, or that patent license was granted, prior to 28 March 2007.</p>
+<pre>Nothing in this License shall be construed as excluding or limiting</pre>
+<p>any implied license or other defenses to infringement that may otherwise be
+available to you under applicable patent law.</p>
+<pre>12. No Surrender of Others&#39; Freedom.
+If conditions are imposed on you (whether by court order, agreement or</pre>
+<p>otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.</p>
+<pre>13. Use with the GNU Affero General Public License.
+Notwithstanding any other provision of this License, you have</pre>
+<p>permission to link or combine any covered work with a work licensed under
+version 3 of the GNU Affero General Public License into a single combined
+work, and to convey the resulting work.  The terms of this License will
+continue to apply to the part which is the covered work, but the special
+requirements of the GNU Affero General Public License, section 13,
+concerning interaction through a network will apply to the combination as
+such.</p>
+<pre>14. Revised Versions of this License.
+The Free Software Foundation may publish revised and/or new versions of</pre>
+<p>the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.</p>
+<pre>Each version is given a distinguishing version number.  If the</pre>
+<p>Program specifies that a certain numbered version of the GNU General Public
+License “or any later version” applies to it, you have the option of
+following the terms and conditions either of that numbered version or of
+any later version published by the Free Software Foundation.  If the
+Program does not specify a version number of the GNU General Public
+License, you may choose any version ever published by the Free Software
+Foundation.</p>
+<pre>If the Program specifies that a proxy can decide which future</pre>
+<p>versions of the GNU General Public License can be used, that proxy&#39;s
+public statement of acceptance of a version permanently authorizes you to
+choose that version for the Program.</p>
+<pre>Later license versions may give you additional or different</pre>
+<p>permissions.  However, no additional obligations are imposed on any author
+or copyright holder as a result of your choosing to follow a later version.</p>
+<pre>15. Disclaimer of Warranty.
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY</pre>
+<p>APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
+<pre>16. Limitation of Liability.
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING</pre>
+<p>WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.</p>
+<pre>17. Interpretation of Sections 15 and 16.
+If the disclaimer of warranty and limitation of liability provided</pre>
+<p>above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates an
+absolute waiver of all civil liability in connection with the Program,
+unless a warranty or assumption of liability accompanies a copy of the
+Program in return for a fee.</p>
+<pre>                   END OF TERMS AND CONDITIONS
+          How to Apply These Terms to Your New Programs
+If you develop a new program, and you want it to be of the greatest</pre>
+<p>possible use to the public, the best way to achieve this is to make it free
+software which everyone can redistribute and change under these terms.</p>
+<pre>To do so, attach the following notices to the program.  It is safest</pre>
+<p>to attach them to the start of each source file to most effectively state
+the exclusion of warranty; and each file should have at least the
+“copyright” line and a pointer to where the full notice is found.</p>
+<pre>&lt;one line to give the program&#39;s name and a brief idea of what it does.&gt;
+Copyright (C) &lt;year&gt;  &lt;name of author&gt;
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</pre>
+<p>Also add information on how to contact you by electronic and paper mail.</p>
+<pre>If the program does terminal interaction, make it output a short</pre>
+<p>notice like this when it starts in an interactive mode:</p>
+<pre>&lt;program&gt;  Copyright (C) &lt;year&gt;  &lt;name of author&gt;
+This program comes with ABSOLUTELY NO WARRANTY; for details type `show w&#39;.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type `show c&#39; for details.</pre>
+<p>The hypothetical commands `show w&#39; and `show c&#39; should show the
+appropriate parts of the General Public License.  Of course, your
+program&#39;s commands might be different; for a GUI interface, you would
+use an “about box”.</p>
+<pre>You should also get your employer (if you work as a programmer) or school,</pre>
+<p>if any, to sign a “copyright disclaimer” for the program, if necessary. For
+more information on this, and how to apply and follow the GNU GPL, see
+&lt;<a href="http://www.gnu.org/licenses">www.gnu.org/licenses</a>/&gt;.</p>
+<pre>The GNU General Public License does not permit incorporating your program</pre>
+<p>into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read &lt;<a
+href="http://www.gnu.org/philosophy/why-not-lgpl.html">www.gnu.org/philosophy/why-not-lgpl.html</a>&gt;.</p>
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