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<h3>
Aaron M. Ucko pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ncbi-entrez-direct">Debian Med / ncbi-entrez-direct</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/566f983fcc9f2297bc10c3752175f616abc185f4">566f983f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T02:17:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.5.20181205+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/11778b936aaa8c19f86842f584a8e5616ce9a7a9">11778b93</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T02:22:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.6.20181210+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/f8c4a9ae74d43fd1c3500bee2635b8f77d86eec6">f8c4a9ae</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:04:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.6.20190103+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/12290890bc12170a932ec141b1f3090e96b8001d">12290890</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:10:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.7.20190104+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/1ce3c44a56495c52c32454db5c78392d3ed66399">1ce3c44a</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:12:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.7.20190114+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/4357532bd4f21699ac294526559c4d3475f2923c">4357532b</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:15:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.8.20190117+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/093bb44f44b9ec9dda575aaae60817c0a16eef44">093bb44f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:25:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.8.20190128+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/492cba4e7c2d8c9ef3a853fd24e062df6cb08aaa">492cba4e</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:38:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.9.20190131+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/commit/1c42e99e91bbfb976d95038ed72113cc6d224482">1c42e99e</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2019-02-07T03:39:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 10.9.20190205+ds</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
</a>
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<li class="file-stats">
<a href="#5f1b2719eaeaeb49bcc6004c5e3f62c796fca4df">
archive-pubmed
</a>
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<li class="file-stats">
<a href="#171e15263cf63f1b48d0cd66342b9fe06d0a729f">
edirect.pl
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<li class="file-stats">
<a href="#6d992cfe40999b8275e4d7351563ea4a41dcec5c">
index-pubmed
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<a href="#eee670f25204100a6fabcf3a1caf31b48e8e2c61">
<span class="deleted-file">
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local-phrase-search
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<a href="#0aae011363caa6b0a509245f540cbd08b70f0d78">
nquire
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<a href="#c352328f4ee63c03c5040ae93a0eb830264a05b8">
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pm-clean
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<a href="#cf42ceaa50c4e25d98dbe78f90643cc3e9d86e12">
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pm-current
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pm-erase
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<a href="#11e69d8774031d4963ce336f99d8a3eb59178485">
pm-index
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pm-log
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pm-repack
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<a href="#386185b94119409d5ca96da9f7d8ec512015a779">
pm-stash
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<a href="#11f18d3ab727247f23018b716384d2eef6c29bd8">
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pm-uids
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pm-verify
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<li class="file-stats">
<a href="#bc3afcd0e5aadf4b16071e20877f44f4d2834572">
rchive.go
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<li class="file-stats">
<a href="#90381f4e965b1aea947ce9f0d8cccfdbe4d1d611">
setup-deps.pl
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<li class="file-stats">
<a href="#a1f9c9e5796fffc51dc6a65b98226224c5841aca">
test-pubmed-index
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<a href="#f3da8dd1a5c431b81c7fe5222e4dfa4856aa8d01">
transmute
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<li class="file-stats">
<a href="#96f5584f0d6dcaca2b56481ad25dbd045758ed30">
xtract.go
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="69e27356ef629022720d868ab0c0e3394775b6c1">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ENTREZ DIRECT<span class="idiff left right"> - README</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ENTREZ DIRECT<span class="idiff left right">: COMMAND LINE ACCESS TO NCBI ENTREZ DATABASES</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected Entrez databases (publication, nucleotide, protein, structure, gene, variation, expression, etc.) from a terminal window. It uses command-line arguments for the query terms and combines individual operations with UNIX pipes</span>.</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">Searching, retrieving, and parsing data from NCBI databases through the Unix command line</span>.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in XML format. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">INTRODUCTION</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">E<span class="idiff left right">Direct consists of a set of scripts that are downloaded to the user's computer. If you extract the archive in your home directory, you may need to enter:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">E<span class="idiff left right">ntrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (biomedical literature, nucleotide and protein sequence, molecular structure, gene, genome assembly, gene expression, clinical variation, etc.) from a Unix terminal window. Search terms are given in command-line arguments. Individual operations are connected with Unix pipes to allow construction of multi-step queries. Selected records can then be retrieved in a variety of formats.</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"><span class="idiff left right"> PATH=$PATH:$HOME/edirect</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">EDirect also includes an argument-driven function that simplifies the extraction of data from document summaries or other results that are in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and Unix utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">in a terminal window to temporarily add EDirect functions to the PATH environment variable so they can be run by name. You can then try EDirect by copying the sample query below and pasting it into the terminal window for execution:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">PROGRAMMATIC ACCESS</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> esearch -db pubmed -query "Beadle AND Tatum AND Neurospora" |</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Several underlying network services provide access to different facets of Entrez. These include searching by indexed terms, looking up precomputed neighbors or links, filtering results by date or category, and downloading record summaries or reports. The same functionalities are available on the web or when using programmatic methods.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">EDirect navigation programs (esearch, elink, efilter, and efetch) communicate by means of a small structured message, which can be passed invisibly between operations with a Unix pipe. The message includes the current database, so it does not need to be given as an argument after the first step.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">All EDirect commands are designed to work on large sets of data. There is no need to write a script to loop over records one at a time. Intermediate results are stored on the Entrez history server. For best performance, obtain an API Key from NCBI, and place the following line in your .bash_profile file:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> export NCBI_API_KEY=user_api_key_goes_here</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Each program also has a -help command that prints detailed information about available arguments.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">NAVIGATION FUNCTIONS</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Esearch performs a new Entrez search using terms in indexed fields. It requires a -db argument for the database name and uses -query to obtain the search terms. For PubMed, without field qualifiers, the server uses automatic term mapping to compose a search strategy by translating the supplied query:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> esearch -db pubmed -query "selective serotonin reuptake inhibitor"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Search terms can be also qualified with bracketed field names:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> esearch -db nucleotide -query "insulin [PROT] AND rodents [ORGN]"</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Elink looks up precomputed neighbors within a database, or finds associated records in other databases:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> elink -related</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> elink -target gene</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Efilter limits the results of a previous query, with shortcuts that can also be used in esearch:</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> efilter -molecule genomic -location chloroplast -country sweden</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Efetch downloads selected records or reports in a designated format:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> efetch -format abstract</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">ENTREZ EXPLORATION</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Individual query commands are connected by a Unix vertical bar pipe symbol:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> esearch -db pubmed -query "transposition immunity" | efetch -format medline</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">PubMed related articles are calculated by a statistical algorithm using the title, abstract, and medical subject headings (MeSH terms). These connections between papers can be used for knowledge discovery.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Lycopene cyclase converts lycopene to beta-carotene, the immediate precursor of vitamin A. An initial search on the enzyme results in 232 articles. Looking up precomputed neighbors returns 14,387 PubMed papers, some of which might be expected to discuss adjacent steps in the biosynthetic pathway:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> esearch -db pubmed -query "lycopene cyclase" |</span>
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14
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> elink -related |</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> efilter -query "NOT historical article [FILT]" |</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> efetch -format docsum |</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> xtract -pattern DocumentSummary -if Author -and Title \</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> -element Id -first "Author/Name" -element Title |</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> grep -i -e enzyme -e synthesis |</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> sort -t $'\t' -k 2,3f |</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> column -s $'\t' -t |</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> head -n 10 |</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> cut -c 1-80</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">This query returns the PubMed ID, first author name, and article title for PubMed "neighbors" (related citations) of the original publications. It then requires specific words in the resulting rows, sorts alphabetically by author name and title, aligns the columns, and truncates the lines for easier viewing:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> 2960822 Anton IA A eukaryotic repressor protein, the qa-1S gene prod</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> 5264137 Arroyo-Begovich A In vitro formation of an active multienzyme complex</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> 14942736 BONNER DM Gene-enzyme relationships in Neurospora.</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> 5361218 Caroline DF Pyrimidine synthesis in Neurospora crassa: gene-enz</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> 123642 Case ME Genetic evidence on the organization and action of </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> elink -target protein |</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> efilter -organism mouse |</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> efetch -format fasta</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Linking to the protein database finds 251,887 sequence records, each of which has standardized organism information from the NCBI taxonomy. Limiting to proteins in mice returns 39 records. (Animals do not encode the genes involved in carotene biosynthesis.) Records are then retrieved in FASTA format. As anticipated, the results include the enzyme that splits beta-carotene into two molecules of retinal:</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> ...</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> >NP_067461.2 beta,beta-carotene 15,15'-dioxygenase isoform 1 [Mus musculus]</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> MEIIFGQNKKEQLEPVQAKVTGSIPAWLQGTLLRNGPGMHTVGESKYNHWFDGLALLHSFSIRDGEVFYR</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> SKYLQSDTYIANIEANRIVVSEFGTMAYPDPCKNIFSKAFSYLSHTIPDFTDNCLINIMKCGEDFYATTE</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> TNYIRKIDPQTLETLEKVDYRKYVAVNLATSHPHYDEAGNVLNMGTSVVDKGRTKYVIFKIPATVPDSKK</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> KGKSPVKHAEVFCSISSRSLLSPSYYHSFGVTENYVVFLEQPFKLDILKMATAYMRGVSWASCMSFDRED</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> KTYIHIIDQRTRKPVPTKFYTDPMVVFHHVNAYEEDGCVLFDVIAYEDSSLYQLFYLANLNKDFEEKSRL</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> TSVPTLRRFAVPLHVDKDAEVGSNLVKVSSTTATALKEKDGHVYCQPEVLYEGLELPRINYAYNGKPYRY</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> IFAAEVQWSPVPTKILKYDILTKSSLKWSEESCWPAEPLFVPTPGAKDEDDGVILSAIVSTDPQKLPFLL</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> ILDAKSFTELARASVDADMHLDLHGLFIPDADWNAVKQTPAETQEVENSDHPTDPTAPELSHSENDFTAG</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> HGGSSL</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> ...</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">STRUCTURED DATA EXTRACTION</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">The xtract program uses command-line arguments to direct the conversion of XML data into a tab-delimited table. The -pattern argument divides the results into rows, while placement of data into columns is controlled by -element.</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">Formatting arguments allow extensive customization of the output. The line break between -pattern objects can be changed with -ret, and the tab character between -element fields can be replaced by -tab.</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">The -sep argument is used to distinguish multiple elements of the same type, and controls their separation independently of the -tab argument. The -sep value also applies to unrelated -element arguments that are grouped with commas. The query:</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> efetch -db pubmed -id 6271474,1413997,16589597 -format docsum |</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> xtract -pattern DocumentSummary -sep "|" -element Id PubDate Name</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">returns a table with individual author names separated by vertical bars:</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> 6271474 1981 Casadaban MJ|Chou J|Lemaux P|Tu CP|Cohen SN</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> 1413997 1992 Oct Mortimer RK|Contopoulou CR|King JS</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> 16589597 1954 Dec Garber ED</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Selection arguments are specialized derivatives of -element. Among these are positional commands (-first and -last) and numeric processing operations (including -num, -len, -sum, -min, -max, and -avg). There are also functions that perform sequence coordinate conversion (-0-based, -1-based, and -ucsc-based).</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">NESTED EXPLORATION</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">Exploration arguments (-pattern, -group, -block, and -subset) limit data extraction to specified regions of the XML, visiting all relevant objects one at a time. This design allows nested exploration of complex, hierarchical data to be controlled by a linear chain of command-line argument statements.</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">PubmedArticle XML contains the MeSH terms applied to a publication. Each MeSH term can have its own unique set of qualifiers. A single level of nested exploration within the current pattern:</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> esearch -db gene -query "beta-carotene oxygenase 1" -organism human |</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> elink -target pubmed | efilter -released last_year | efetch -format xml |</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> xtract -pattern PubmedArticle -element MedlineCitation/PMID \</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> -block MeshHeading \</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> -pfc "\n" -sep "/" -element DescriptorName,QualifierName</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">retains the proper association of subheadings for each MeSH term:</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> 30396924</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> Age Factors</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> Animals</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> Cell Cycle Proteins/deficiency/genetics/metabolism</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> Cellular Senescence/physiology</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> ...</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">CONDITIONAL EXECUTION</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">Conditional processing arguments (-if and -unless) restrict exploration by object name and value. These may be used in conjunction with string or numeric constraints:</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> esearch -db pubmed -query "Casadaban MJ [AUTH]" |</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> efetch -format xml |</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> xtract -pattern PubmedArticle -if "#Author" -lt 6 \</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> -block Author -if LastName -is-not Casadaban \</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> -sep ", " -tab "\n" -element LastName,Initials |</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> sort-uniq-count-rank</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">to select papers with fewer than 6 authors and print a table of the most frequent coauthors:</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> 11 Chou, J</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> 8 Cohen, SN</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> 7 Groisman, EA</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> ...</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">SAVING DATA IN VARIABLES</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">A value can be recorded in a variable and used wherever needed. Variables are created by a hyphen followed by a name consisting of a string of capital letters or digits (e.g., -PMID). Values are retrieved by placing an ampersand before the variable name (e.g., "&PMID") in an -element statement:</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> efetch -db pubmed -id 3201829,6301692,781293 -format xml |</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> xtract -pattern PubmedArticle -PMID MedlineCitation/PMID \</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> -block Author -element "&PMID" \</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> -sep " " -tab "\n" -element Initials,LastName</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">producing a list of authors, with the PubMed Identifier (PMID) in the first column of each row:</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> 3201829 JR Johnston</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> 3201829 CR Contopoulou</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> 3201829 RK Mortimer</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> 6301692 MA Krasnow</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> 6301692 NR Cozzarelli</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> 781293 MJ Casadaban</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">The variable can be used even though the original object is no longer visible inside the -block section.</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">SEQUENCE QUALIFIERS</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">The NCBI represents sequence records in a data model based on the central dogma of molecular biology. A sequence can have multiple features, which carry information about the biology of a given region, including the transformations involved in gene expression. A feature can have multiple qualifiers, which store specific details about that feature (e.g., name of the gene, genetic code used for translation).</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">The data hierarchy is easily explored using a -pattern {sequence} -group {feature} -block {qualifier} construct. As a convenience, an -insd helper function is provided for generating the appropriate nested extraction commands from feature and qualifier names on the command line. Processing the results of a search on cone snail venom:</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> esearch -db protein -query "conotoxin" -feature mat_peptide |</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> efetch -format gpc |</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> xtract -insd complete mat_peptide "%peptide" product peptide |</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> grep -i conotoxin | sort -t $'\t' -u -k 2,2n</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">returns the accession, length, name, and sequence for a sample of neurotoxic peptides:</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> ADB43131.1 15 conotoxin Cal 1b LCCKRHHGCHPCGRT</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> ADB43128.1 16 conotoxin Cal 5.1 DPAPCCQHPIETCCRR</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> AIC77105.1 17 conotoxin Lt1.4 GCCSHPACDVNNPDICG</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> ADB43129.1 18 conotoxin Cal 5.2 MIQRSQCCAVKKNCCHVG</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> ADD97803.1 20 conotoxin Cal 1.2 AGCCPTIMYKTGACRTNRCR</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> AIC77085.1 21 conotoxin Bt14.8 NECDNCMRSFCSMIYEKCRLK</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> ADB43125.1 22 conotoxin Cal 14.2 GCPADCPNTCDSSNKCSPGFPG</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> AIC77154.1 23 conotoxin Bt14.19 VREKDCPPHPVPGMHKCVCLKTC</span>
</pre>
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32
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> ...</span>
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33
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">EDirect will run on UNIX and Macintosh computers that have the Perl language installed, and under the Cygwin UNIX-emulation environment on Windows PCs.</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">INSTALLATION</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">EDirect consists of a set of scripts and programs that are downloaded to the user's computer.</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">EDirect will run on Unix and Macintosh computers that have the Perl language installed, and under the Cygwin Unix-emulation environment on Windows PCs.</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">To install the EDirect software, copy the following commands and paste them into a terminal window:</span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"></span>
</pre>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> cd ~</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> /bin/bash</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> perl -MNet::FTP -e \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> $ftp->login; $ftp->binary;</span>
</pre>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> $ftp->get("/entrez/entrezdirect/edirect.tar.gz");'</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> gunzip -c edirect.tar.gz | tar xf -</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> rm edirect.tar.gz</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> builtin exit</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect"</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> ./edirect/setup.sh</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">This downloads several scripts into an "edirect" folder in the user's home directory. The setup.sh script then downloads any missing Perl modules, and may print an additional command for updating the PATH environment variable in the user's configuration file. Copy that command, if present, and paste it into the terminal window to complete the installation process. The editing instructions will look something like:</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> echo "export PATH=\$PATH:\$HOME/edirect" >> $HOME/.bash_profile</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">DOCUMENTATION</span>
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35
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext"></span>
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36
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">Documentation for EDirect is on the web at:</span>
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37
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext"> http://www.ncbi.nlm.nih.gov/books/NBK179288</span>
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39
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Questions or comments on EDirect may be sent to eutilities@ncbi.nlm.nih.gov.</span></pre>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">Information on how to obtain an API Key is described in this NCBI blogpost:</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">Questions or comments on EDirect may be sent to info@ncbi.nlm.nih.gov.</span></pre>
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<li id="5f1b2719eaeaeb49bcc6004c5e3f62c796fca4df">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#5f1b2719eaeaeb49bcc6004c5e3f62c796fca4df"><strong>archive-pubmed</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ if [ "$#" -gt 0 ]</td>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="nv" style="color: teal;">MASTER</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span><span class="k" style="font-weight: 600;">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">CONFIG</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">MASTER</span><span class="k" style="font-weight: 600;">}</span></span>
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24
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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25
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_PUBMED_MASTER</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +71,7 @@ do</td>
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70
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MASTER</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"></span>
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73
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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="nb" style="color: #0086b3;">dir </span><span class="k" style="font-weight: 600;">in </span><span class="idiff left right">Current </span>Indexed Inverted Merged Pubmed</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="nb" style="color: #0086b3;">dir </span><span class="k" style="font-weight: 600;">in </span>Indexed Inverted Merged Pubmed</span>
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74
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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76
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,3 +99,20 @@ fetch-pubmed -path "$MASTER/Archive" |</td>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="shell">xtract <span class="nt" style="color: navy;">-pattern</span> Author <span class="nt" style="color: navy;">-if</span> Affiliation <span class="nt" style="color: navy;">-contains</span> Medicine <span class="se" style="color: #d14;">\</span></span>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"> <span class="nt" style="color: navy;">-pfx</span> <span class="s2" style="color: #d14;">"Archive is "</span> <span class="nt" style="color: navy;">-element</span> Initials</span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$CONFIG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span>bash_profile</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$HOME</span><span class="s2" style="color: #d14;">/.bashrc"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$HOME</span>/.<span class="nv" style="color: teal;">$target</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'bashrc'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$HOME</span><span class="s2" style="color: #d14;">/.</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span>bashrc</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"For convenience, please execute the following to save the archive path to a variable:"</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" echo </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">export EDIRECT_PUBMED_MASTER='</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CONFIG</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> >>"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">HOME/.</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ use File::Spec;</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># EDirect version number</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">5</span>"</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">9</span>"</span><span class="p">;</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"></span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">BEGIN</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,6 +116,7 @@ sub clearflags {</td>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"> <span class="nv" style="color: teal;">$batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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117
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"> <span class="nv" style="color: teal;">$chr_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"> <span class="nv" style="color: teal;">$chr_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="perl"> <span class="nv" style="color: teal;">$class</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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119
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="perl"> <span class="nv" style="color: teal;">$clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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120
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"> <span class="nv" style="color: teal;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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121
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"> <span class="nv" style="color: teal;">$compact</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,6 +144,7 @@ sub clearflags {</td>
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143
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="perl"> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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144
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="perl"> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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145
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="perl"> <span class="nv" style="color: teal;">$input</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl"> <span class="nv" style="color: teal;">$internal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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146
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="perl"> <span class="nv" style="color: teal;">$journal</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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147
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="perl"> <span class="nv" style="color: teal;">$json</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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148
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="perl"> <span class="nv" style="color: teal;">$just_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -170,6 +172,7 @@ sub clearflags {</td>
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170
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="perl"> <span class="nv" style="color: teal;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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171
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="perl"> <span class="nv" style="color: teal;">$raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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172
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="perl"> <span class="nv" style="color: teal;">$related</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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173
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="perl"> <span class="nv" style="color: teal;">$rldate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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175
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq_stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,6 +195,7 @@ sub clearflags {</td>
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192
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="perl"> <span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
193
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="perl"> <span class="nv" style="color: teal;">$volume</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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194
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="perl"> <span class="nv" style="color: teal;">$web</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="perl"> <span class="nv" style="color: teal;">$released</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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195
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="perl"> <span class="nv" style="color: teal;">$word</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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196
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="perl"> <span class="nv" style="color: teal;">$year</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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197
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -210,10 +214,20 @@ sub clearflags {</td>
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210
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="perl"></span>
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211
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"> <span class="nv" style="color: teal;">$api_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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212
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="perl"> <span class="nv" style="color: teal;">$api_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ENV</span><span class="p">{</span><span class="nv" style="color: teal;">NCBI_API_KEY</span><span class="p">}</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$ENV</span><span class="p">{</span><span class="nv" style="color: teal;">NCBI_API_KEY</span><span class="p">};</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="perl"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"> <span class="nv" style="color: teal;">$abbrv_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$ENV</span><span class="p">{</span><span class="nv" style="color: teal;">EDIRECT_DO_AUTO_ABBREV</span><span class="p">}</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$ENV</span><span class="p">{</span><span class="nv" style="color: teal;">EDIRECT_DO_AUTO_ABBREV</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"true"</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"> <span class="nv" style="color: teal;">$abbrv_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">true</span><span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="perl"> <span class="p">}</span></span>
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213
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="perl"><span class="p">}</span></span>
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214
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="perl"></span>
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215
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">do_sleep</span> <span class="p">{</span></span>
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216
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$internal</span> <span class="p">)</span> <span class="p">{</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="perl"> <span class="nn" style="color: #555;">Time::HiRes::</span><span class="nv" style="color: teal;">usleep</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl"> <span class="p">}</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="perl"></span>
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217
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$api_key</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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218
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$log</span> <span class="p">)</span> <span class="p">{</span></span>
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219
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"sleeping 1/10 second\n"</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -360,8 +374,17 @@ sub read_aliases {</td>
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360
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="perl"></span>
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361
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">adjust_base</span> <span class="p">{</span></span>
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362
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="perl"></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$basx</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="perl"> <span class="nv" style="color: teal;">$internal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="perl"> <span class="p">}</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="perl"></span>
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363
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$basx</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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364
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$internal</span> <span class="p">)</span> <span class="p">{</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="perl"> <span class="nv" style="color: teal;">$base</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://eutils-internal.ncbi.nlm.nih.gov/entrez/eutils/"</span><span class="p">;</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="perl"> <span class="p">}</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="perl"></span>
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365
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if base not overridden, check URL of previous query, stick with main or colo site,</span></span>
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366
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># since history server data for EUtils does not copy between locations, by design</span></span>
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367
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -512,12 +535,14 @@ sub get_count {</td>
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512
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="perl"> <span class="nv" style="color: teal;">$output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">get</span> <span class="p">(</span><span class="nv" style="color: teal;">$url</span><span class="p">);</span></span>
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513
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="perl"></span>
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514
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$output</span> <span class="p">)</span> <span class="p">{</span></span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of '$url'\n"</span><span class="p">;</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of get_count '$url'\n"</span><span class="p">;</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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516
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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517
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="perl"> <span class="p">}</span></span>
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518
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="perl"></span>
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519
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$output</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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520
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"No get_count output returned from '$url'\n"</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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521
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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522
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="perl"> <span class="p">}</span></span>
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523
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -531,10 +556,12 @@ sub get_count {</td>
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531
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="perl"></span>
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532
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$errx</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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533
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="p">(</span><span class="bp" style="color: #999;">STDOUT</span><span class="p">);</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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534
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"ERROR in count output: $errx\nURL: $url\n\n"</span><span class="p">;</span></span>
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535
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="perl"> <span class="p">}</span></span>
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536
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="perl"></span>
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537
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$numx</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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538
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Count value not found in count output - WebEnv $webx\n"</span><span class="p">;</span></span>
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539
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="perl"> <span class="p">}</span></span>
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540
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -607,7 +634,8 @@ sub get_uids {</td>
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607
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$data</span> <span class="p">)</span> <span class="p">{</span></span>
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608
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="perl"> <span class="nv" style="color: teal;">$keep_trying</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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609
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of '$url'\n"</span><span class="p">;</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of get_uids '$url'\n"</span><span class="p">;</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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611
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639
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="perl"> <span class="p">}</span></span>
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612
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="perl"> <span class="p">}</span></span>
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613
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641
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$keep_trying</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -687,12 +715,14 @@ sub do_post_yielding_ref {</td>
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687
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="perl"> <span class="nv" style="color: teal;">$rslt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">get</span> <span class="p">(</span><span class="nv" style="color: teal;">$urlx</span><span class="p">);</span></span>
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688
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="perl"></span>
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689
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$rslt</span> <span class="p">)</span> <span class="p">{</span></span>
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690
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of '$urlx'\n"</span><span class="p">;</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of do_get '$urlx'\n"</span><span class="p">;</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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691
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<td class="diff-line-num new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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692
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
693
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<td class="diff-line-num new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
694
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<td class="diff-line-num new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$rslt</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
695
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<td class="diff-line-num new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"No do_get output returned from '$urlx'\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
696
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<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
697
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<td class="diff-line-num new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
698
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<td class="diff-line-num new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
728
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -717,7 +747,15 @@ sub do_post_yielding_ref {</td>
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717
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<td class="diff-line-num new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$res</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">is_success</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
718
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<td class="diff-line-num new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="perl"> <span class="nv" style="color: teal;">$rslt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$res</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">content_ref</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
719
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<td class="diff-line-num new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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720
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<td class="diff-line-num new_line old" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: teal;">$res</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">status_line</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="perl"> <span class="nv" style="color: teal;">$stts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$res</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">status_line</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nv" style="color: teal;">$stts</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$stts</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"429 Too Many Requests"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$api_key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"PLEASE REQUEST AN API_KEY FROM NCBI\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"TOO MANY REQUESTS EVEN WITH API_KEY\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="perl"> <span class="p">}</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="perl"> <span class="p">}</span></span>
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721
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="perl"> <span class="p">}</span></span>
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722
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="perl"></span>
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723
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$$rslt</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1052,12 +1090,32 @@ sub write_edirect {</td>
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1052
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="perl"></span>
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1053
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1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># wrapper to detect command line errors</span></span>
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1054
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="perl"></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$abbrev_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qq{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="perl"><span class="sx" style="color: #d14;"> To enable argument auto abbreviation resolution, run:</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="perl"></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="perl"><span class="sx" style="color: #d14;"> export EDIRECT_DO_AUTO_ABBREV="true"</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="perl"></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="perl"><span class="sx" style="color: #d14;"> in the terminal, or add that line to your .bash_profile configuration file.</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="perl"></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="perl"><span class="sx" style="color: #d14;">}</span><span class="p">;</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="perl"></span>
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1055
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">MyGetOptions</span> <span class="p">{</span></span>
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1056
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1057
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$help_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
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1058
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="perl"></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$abbrv_flag</span> <span class="p">)</span> <span class="p">{</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="perl"> <span class="nn" style="color: #555;">Getopt::Long::</span><span class="nv" style="color: teal;">Configure</span><span class="p">(</span><span class="s" style="color: #d14;">"auto_abbrev"</span><span class="p">);</span></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="perl"> <span class="nn" style="color: #555;">Getopt::Long::</span><span class="nv" style="color: teal;">Configure</span><span class="p">(</span><span class="s" style="color: #d14;">"no_auto_abbrev"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="perl"></span>
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1059
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<td class="diff-line-num new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">GetOptions</span><span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1060
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<td class="diff-line-num new_line old" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="nv" style="color: teal;">$help_msg</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$abbrv_flag</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="nv" style="color: teal;">$help_msg</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$help_msg</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="nv" style="color: teal;">$abbrev_help</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1062
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<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="p">(</span><span class="s" style="color: #d14;">"Entrez Direct does not support positional arguments.\n"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="perl"> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"Please remember to quote parameter values containing\n"</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1089,6 +1147,7 @@ sub ecntc {</td>
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<td class="diff-line-num old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1089
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<td class="diff-line-num new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1090
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<td class="diff-line-num new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1091
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<td class="diff-line-num new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1092
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<td class="diff-line-num new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1151
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1151" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1093
</td>
<td class="diff-line-num new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1094
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<td class="diff-line-num new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1153
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1153" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1151,8 +1210,10 @@ Spell Check</td>
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1151
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<td class="diff-line-num new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="perl"><span class="sx" style="color: #d14;">Publication Filters</span></span>
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<td class="diff-line-num old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1152
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<td class="diff-line-num new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1153
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<td class="diff-line-num new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="perl"><span class="sx" style="color: #d14;"> -pub abstract, clinical, english, free, historical,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1154
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<td class="diff-line-num new_line old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1154" class="line" lang="perl"><span class="sx" style="color: #d14;"> journal, last_week, last_month, last_year,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1155
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<td class="diff-line-num new_line old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1155" class="line" lang="perl"><span class="sx" style="color: #d14;"> medline, preprint, published, review, structured</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="perl"><span class="sx" style="color: #d14;"> journal, medline, preprint, published, review,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="perl"><span class="sx" style="color: #d14;"> structured</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="perl"><span class="sx" style="color: #d14;"> -journal pnas, "j bacteriol", ...</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="perl"><span class="sx" style="color: #d14;"> -released last_week, last_month, last_year, prev_years</span></span>
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<td class="diff-line-num old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<td class="diff-line-num new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1157
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<td class="diff-line-num new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="perl"><span class="sx" style="color: #d14;">Sequence Filters</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1158
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<td class="diff-line-num new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1170,6 +1231,11 @@ Gene Filters</td>
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1170
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<td class="diff-line-num new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="perl"><span class="sx" style="color: #d14;"> -status alive</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1171
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<td class="diff-line-num new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1232
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1232" class="line" lang="perl"><span class="sx" style="color: #d14;"> -type coding, pseudo</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1172
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<td class="diff-line-num new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="perl"><span class="sx" style="color: #d14;">SNP Filters</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="perl"><span class="sx" style="color: #d14;"> -class acceptor, donor, frameshift, indel, intron,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="perl"><span class="sx" style="color: #d14;"> missense, nonsense, synonymous</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1173
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<td class="diff-line-num new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="perl"><span class="sx" style="color: #d14;">Miscellaneous Arguments</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1174
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<td class="diff-line-num new_line" data-linenumber="1240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1175
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<td class="diff-line-num new_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="perl"><span class="sx" style="color: #d14;"> -label Alias for query step</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1180,6 +1246,8 @@ sub process_extras {</td>
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1180
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<td class="diff-line-num new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1181
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<td class="diff-line-num new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$frst</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1182
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<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$publ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rlsd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$jrnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1183
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<td class="diff-line-num new_line" data-linenumber="1251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ctry</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1184
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<td class="diff-line-num new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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<td class="diff-line-num new_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$locn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1188,8 +1256,11 @@ sub process_extras {</td>
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<td class="diff-line-num old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1188
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<td class="diff-line-num new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sorc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1189
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<td class="diff-line-num new_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1257
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="diff-line-num new_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1258
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<pre style="margin: 0;"> <span id="LC1258" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$gtyp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$clss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<td class="diff-line-num new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<td class="diff-line-num new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="perl"> <span class="nv" style="color: teal;">$publ</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$publ</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="perl"> <span class="nv" style="color: teal;">$rlsd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$rlsd</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="perl"> <span class="nv" style="color: teal;">$jrnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$jrnl</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1193
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<td class="diff-line-num new_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="perl"> <span class="nv" style="color: teal;">$ctry</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$ctry</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1194
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<td class="diff-line-num new_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="perl"> <span class="nv" style="color: teal;">$fkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$fkey</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1195
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<td class="diff-line-num new_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="perl"> <span class="nv" style="color: teal;">$bmol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$bmol</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1198,6 +1269,7 @@ sub process_extras {</td>
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1198
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<td class="diff-line-num new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="perl"> <span class="nv" style="color: teal;">$sorc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$sorc</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1199
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<td class="diff-line-num new_line" data-linenumber="1270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1270
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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="perl"> <span class="nv" style="color: teal;">$stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$stat</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1200
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<td class="diff-line-num new_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1271
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="perl"> <span class="nv" style="color: teal;">$gtyp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$gtyp</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="perl"> <span class="nv" style="color: teal;">$clss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$clss</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1201
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<td class="diff-line-num new_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1202
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<td class="diff-line-num new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">pubHash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1203
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<td class="diff-line-num new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="perl"> <span class="s" style="color: #d14;">'abstract'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'has abstract [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1219,6 +1291,15 @@ sub process_extras {</td>
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<td class="diff-line-num old_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<td class="diff-line-num new_line" data-linenumber="1291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="perl"> <span class="s" style="color: #d14;">'trial'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'clinical trial [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1220
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<td class="diff-line-num new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="perl"> <span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<td class="diff-line-num new_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1293
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">releasedHash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="perl"> <span class="s" style="color: #d14;">'last_month'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last month [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="perl"> <span class="s" style="color: #d14;">'last month'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last month [FILT]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="perl"> <span class="s" style="color: #d14;">'last_week'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last week [FILT]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="perl"> <span class="s" style="color: #d14;">'last week'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last week [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="perl"> <span class="s" style="color: #d14;">'last_year'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last year [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="perl"> <span class="s" style="color: #d14;">'last year'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'published last year [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="perl"> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="perl"></span>
</pre>
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1222
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<td class="diff-line-num new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="perl"> <span class="nv" style="color: teal;">@featureArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1223
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<td class="diff-line-num new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="perl"> <span class="s" style="color: #d14;">"-10_signal"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1224
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<td class="diff-line-num new_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="perl"> <span class="s" style="color: #d14;">"-35_signal"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1362,6 +1443,17 @@ sub process_extras {</td>
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1362
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<td class="diff-line-num new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="perl"> <span class="s" style="color: #d14;">'viruses'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'viruses [FILT]'</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1363
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<td class="diff-line-num new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="perl"> <span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1364
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<td class="diff-line-num new_line" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">snpHash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="perl"> <span class="s" style="color: #d14;">'acceptor'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'splice acceptor variant [FXN]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="perl"> <span class="s" style="color: #d14;">'donor'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'splice donor variant [FXN]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="perl"> <span class="s" style="color: #d14;">'frameshift'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'frameshift [FXN]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="perl"> <span class="s" style="color: #d14;">'indel'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'cds indel [FXN]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="perl"> <span class="s" style="color: #d14;">'intron'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'intron [FXN]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="perl"> <span class="s" style="color: #d14;">'missense'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'missense [FXN]'</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="perl"> <span class="s" style="color: #d14;">'nonsense'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'nonsense [FXN]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="perl"> <span class="s" style="color: #d14;">'synonymous'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'synonymous codon [FXN]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="perl"> <span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1365
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<td class="diff-line-num new_line" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">sourceHash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1366
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<td class="diff-line-num new_line" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1458
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1458" class="line" lang="perl"> <span class="s" style="color: #d14;">'ddbj'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'srcdb ddbj [PROP]'</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1367
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<td class="diff-line-num new_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1459" class="line" lang="perl"> <span class="s" style="color: #d14;">'embl'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'srcdb embl [PROP]'</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1387,34 +1479,62 @@ sub process_extras {</td>
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<td class="diff-line-num old_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1387
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<td class="diff-line-num new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1479" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1388
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<td class="diff-line-num new_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1480
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@working</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1389
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<td class="diff-line-num new_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="perl"></span>
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1390
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<td class="diff-line-num new_line old" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1390" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$suffix1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$suffix2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1484
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<pre style="margin: 0;">+<span id="LC1484" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1485
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$is_published</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$is_prev_year</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1391
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<td class="diff-line-num new_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1487
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<pre style="margin: 0;"> <span id="LC1487" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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<td class="diff-line-num new_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$frst</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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<td class="diff-line-num new_line" data-linenumber="1489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1489
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$frst</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<td class="diff-line-num new_line" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1395
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1491
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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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1492
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$publ</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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1397
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$pubHash</span><span class="p">{</span><span class="nv" style="color: teal;">$publ</span><span class="p">}</span> <span class="p">)</span> <span class="p">{</span></span>
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1398
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<td class="diff-line-num new_line old" data-linenumber="1493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$pubHash</span><span class="p">{</span><span class="nv" style="color: teal;">$publ</span><span class="p">};</span></span>
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1493
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># -pub can use comma-separated list</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1494
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@pbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="nv" style="color: teal;">$publ</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: teal;">$pb</span> <span class="p">(</span><span class="nv" style="color: teal;">@pbs</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1496
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$pubHash</span><span class="p">{</span><span class="nv" style="color: teal;">$pb</span><span class="p">}</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$pubHash</span><span class="p">{</span><span class="nv" style="color: teal;">$pb</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pb</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"published"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="perl"> <span class="nv" style="color: teal;">$is_published</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -pub argument '$pb', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$rlsd</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$releasedHash</span><span class="p">{</span><span class="nv" style="color: teal;">$rlsd</span><span class="p">}</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1509
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<pre style="margin: 0;">+<span id="LC1509" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$releasedHash</span><span class="p">{</span><span class="nv" style="color: teal;">$rlsd</span><span class="p">};</span></span>
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1399
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<td class="diff-line-num new_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1510
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1400
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<td class="diff-line-num new_line old" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$<span class="idiff left">publ</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"published</span>"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1401
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<td class="diff-line-num new_line old" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="perl"> <span class="nv" style="color: teal;">$<span class="idiff left">suffix</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"published"</span></span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$<span class="idiff left">rlsd</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"prev_years</span>"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="perl"> <span class="nv" style="color: teal;">$<span class="idiff left">is_prev_year</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">true</span></span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1402
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<td class="diff-line-num new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1403
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<td class="diff-line-num new_line old" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -<span class="idiff left right">pub argument '$publ</span>', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -<span class="idiff left right">released argument '$rlsd</span>', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
</pre>
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1404
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<td class="diff-line-num new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1405
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<td class="diff-line-num new_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<td class="diff-line-num new_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$jrnl</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$jrnl</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" [JOUR]"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1407
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<td class="diff-line-num new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$ctry</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1408
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"country "</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$ctry</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" [TEXT]"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1409
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<td class="diff-line-num new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<pre style="margin: 0;"> <span id="LC1525" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1410
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<td class="diff-line-num new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1411
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<td class="diff-line-num new_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<pre style="margin: 0;"> <span id="LC1527" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<td class="diff-line-num new_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$fkey</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1413
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<td class="diff-line-num new_line old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">grep</span><span class="p">(</span> <span class="sr" style="color: #009926;">/^$fkey$/</span><span class="p">,</span> <span class="nv" style="color: teal;">@featureArray</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1414
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<td class="diff-line-num new_line old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$fkey</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" [FKEY]"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1415
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<td class="diff-line-num new_line old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1416
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<td class="diff-line-num new_line old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1417
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<td class="diff-line-num new_line old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -feature argument '$fkey', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># -feature can use comma-separated list</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@fts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="nv" style="color: teal;">$fkey</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: teal;">$ft</span> <span class="p">(</span><span class="nv" style="color: teal;">@fts</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">grep</span><span class="p">(</span> <span class="sr" style="color: #009926;">/^$ft$/</span><span class="p">,</span> <span class="nv" style="color: teal;">@featureArray</span> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ft</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" [FKEY]"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -feature argument '$ft', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1418
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1538
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1419
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<td class="diff-line-num new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1420
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1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1475,12 +1595,25 @@ sub process_extras {</td>
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1475
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1595
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<pre style="margin: 0;"> <span id="LC1595" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1476
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<td class="diff-line-num new_line" data-linenumber="1596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1477
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<td class="diff-line-num new_line" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1597
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="perl"></span>
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1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$clss</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$snpHash</span><span class="p">{</span><span class="nv" style="color: teal;">$clss</span><span class="p">}</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$snpHash</span><span class="p">{</span><span class="nv" style="color: teal;">$clss</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1601
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<pre style="margin: 0;">+<span id="LC1601" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1602
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1603
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"\nUnrecognized -class argument '$clss', use efilter -help to see available choices\n\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1606
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<pre style="margin: 0;">+<span id="LC1606" class="line" lang="perl"></span>
</pre>
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1478
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<td class="diff-line-num new_line" data-linenumber="1607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$xtras</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span> <span class="p">(</span><span class="s" style="color: #d14;">" AND "</span><span class="p">,</span> <span class="nv" style="color: teal;">@working</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
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<td class="diff-line-num new_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1608
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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1480
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<td class="diff-line-num new_line old" data-linenumber="1609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1480" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$<span class="idiff left">suffix</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"published"</span></span> <span class="p">)</span> <span class="p">{</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$<span class="idiff left right">is_published</span></span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1481
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<td class="diff-line-num new_line" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1610
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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="perl"> <span class="nv" style="color: teal;">$xtras</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$xtras</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" NOT ahead of print [FILT]"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1482
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<td class="diff-line-num new_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1483
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<td class="diff-line-num new_line" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1613
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<pre style="margin: 0;">+<span id="LC1613" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$is_prev_year</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="perl"> <span class="nv" style="color: teal;">$xtras</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$xtras</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">" NOT published last year [FILT]"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1484
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<td class="diff-line-num new_line" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$xtras</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1485
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<td class="diff-line-num new_line" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1486
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<td class="diff-line-num new_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1514,6 +1647,7 @@ sub efilt {</td>
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<td class="diff-line-num old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<td class="diff-line-num new_line" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="perl"> <span class="nv" style="color: teal;">MyGetOptions</span><span class="p">(</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<td class="diff-line-num new_line" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1648
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="perl"> <span class="nv" style="color: teal;">$filt_help</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<td class="diff-line-num new_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="perl"> <span class="s" style="color: #d14;">"query=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1650
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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="perl"> <span class="s" style="color: #d14;">"q=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<td class="diff-line-num new_line" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="perl"> <span class="s" style="color: #d14;">"sort=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$sort</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
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<td class="diff-line-num new_line" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="perl"> <span class="s" style="color: #d14;">"days=i"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$rldate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1519
</td>
<td class="diff-line-num new_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1653
</td>
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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="perl"> <span class="s" style="color: #d14;">"mindate=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$mndate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1523,7 +1657,9 @@ sub efilt {</td>
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<td class="diff-line-num old_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<td class="diff-line-num new_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1657
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<pre style="margin: 0;"> <span id="LC1657" class="line" lang="perl"> <span class="s" style="color: #d14;">"field=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$field</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<td class="diff-line-num new_line" data-linenumber="1658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1658
</td>
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<pre style="margin: 0;"> <span id="LC1658" class="line" lang="perl"> <span class="s" style="color: #d14;">"spell"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$spell</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
</td>
<td class="diff-line-num new_line" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1659
</td>
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="perl"> <span class="s" style="color: #d14;">"pairs=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$pair</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1660
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<pre style="margin: 0;">+<span id="LC1660" class="line" lang="perl"> <span class="s" style="color: #d14;">"journal=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$journal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<td class="diff-line-num new_line" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1661
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1661" class="line" lang="perl"> <span class="s" style="color: #d14;">"pub=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$pub</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1662
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<pre style="margin: 0;">+<span id="LC1662" class="line" lang="perl"> <span class="s" style="color: #d14;">"released=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$released</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<td class="diff-line-num new_line" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1663
</td>
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="perl"> <span class="s" style="color: #d14;">"country=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$country</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<td class="diff-line-num new_line" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1664
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1664" class="line" lang="perl"> <span class="s" style="color: #d14;">"feature=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$feature</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<td class="diff-line-num new_line" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="perl"> <span class="s" style="color: #d14;">"location=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$location</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1532,6 +1668,7 @@ sub efilt {</td>
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<td class="diff-line-num old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1532
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<td class="diff-line-num new_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1668
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1668" class="line" lang="perl"> <span class="s" style="color: #d14;">"source=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$source</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
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<td class="diff-line-num new_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1669
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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="perl"> <span class="s" style="color: #d14;">"status=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$status</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1534
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<td class="diff-line-num new_line" data-linenumber="1670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1670
</td>
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="perl"> <span class="s" style="color: #d14;">"type=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$gtype</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1671
</td>
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<pre style="margin: 0;">+<span id="LC1671" class="line" lang="perl"> <span class="s" style="color: #d14;">"class=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$class</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1535
</td>
<td class="diff-line-num new_line" data-linenumber="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1672
</td>
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="perl"> <span class="s" style="color: #d14;">"api_key=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$api_key</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1536
</td>
<td class="diff-line-num new_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="perl"> <span class="s" style="color: #d14;">"email=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$emaddr</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1537
</td>
<td class="diff-line-num new_line" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1674
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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="perl"> <span class="s" style="color: #d14;">"tool=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$tuul</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1539,6 +1676,7 @@ sub efilt {</td>
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<td class="diff-line-num old_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1539
</td>
<td class="diff-line-num new_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1676
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1676" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1540
</td>
<td class="diff-line-num new_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1677
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1677" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1541
</td>
<td class="diff-line-num new_line" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1678
</td>
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<pre style="margin: 0;"> <span id="LC1678" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1679
</td>
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1542
</td>
<td class="diff-line-num new_line" data-linenumber="1680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1680
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1680" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1543
</td>
<td class="diff-line-num new_line" data-linenumber="1681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1681
</td>
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1544
</td>
<td class="diff-line-num new_line" data-linenumber="1682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1682
</td>
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1554,7 +1692,7 @@ sub efilt {</td>
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1692
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="perl"> <span class="p">}</span></span>
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1555
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1693
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<pre style="margin: 0;"> <span id="LC1693" class="line" lang="perl"></span>
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1556
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1694
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<pre style="margin: 0;"> <span id="LC1694" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># process special filter flags, add to query string</span></span>
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1557
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<pre style="margin: 0;">-<span id="LC1557" class="line" lang="perl"> <span class="nv" style="color: teal;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">process_extras</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span><span class="p">,</span> <span class="nv" style="color: teal;">$pub</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">country</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$feature</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$location</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$molecule</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$organism</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$source</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$status</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$gtype</span></span> <span class="p">);</span></span>
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1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="perl"> <span class="nv" style="color: teal;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">process_extras</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span><span class="p">,</span> <span class="nv" style="color: teal;">$pub</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">released</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$journal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$country</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$feature</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$location</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$molecule</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$organism</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$source</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$status</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$gtype</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$class</span></span> <span class="p">);</span></span>
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="perl"></span>
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1559
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">t</span> <span class="bp" style="color: #999;">STDIN</span> <span class="p">)</span> <span class="p">{</span></span>
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1560
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1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1585,8 +1723,8 @@ sub efilt {</td>
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1585
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1723
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="perl"> <span class="nv" style="color: teal;">$email</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$emaddr</span><span class="p">;</span></span>
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1586
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1724
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<pre style="margin: 0;"> <span id="LC1724" class="line" lang="perl"> <span class="p">}</span></span>
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1587
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1725
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<pre style="margin: 0;"> <span id="LC1725" class="line" lang="perl"></span>
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1588
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<td class="diff-line-num new_line old" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1588" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$rldate</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$mndate</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$mxdate</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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1589
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<pre style="margin: 0;">-<span id="LC1589" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Must supply -query or -days or -mindate and -maxdate arguments on command line\n"</span><span class="p">;</span></span>
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1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$<span class="idiff left">sort</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$</span>rldate</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$mndate</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$mxdate</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Must supply -query or -<span class="idiff left right">sort or -</span>days or -mindate and -maxdate arguments on command line\n"</span><span class="p">;</span></span>
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1590
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1728
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="perl"></span>
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1592
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1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">binmode</span> <span class="bp" style="color: #999;">STDOUT</span><span class="p">,</span> <span class="s" style="color: #d14;">":utf8"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1897,6 +2035,7 @@ sub esmry {</td>
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1897
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$silent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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1898
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<td class="diff-line-num new_line" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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1899
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<td class="diff-line-num new_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$internal</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1900
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2039
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<pre style="margin: 0;"> <span id="LC2039" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$log</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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1901
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2040
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<pre style="margin: 0;"> <span id="LC2040" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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1902
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2041
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<pre style="margin: 0;"> <span id="LC2041" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="p">(</span><span class="nv" style="color: teal;">@_</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2175,6 +2314,7 @@ Format Examples</td>
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2175
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2314
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<pre style="margin: 0;"> <span id="LC2314" class="line" lang="perl"><span class="sx" style="color: #d14;"> summary Summary</span></span>
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2176
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2315
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<pre style="margin: 0;"> <span id="LC2315" class="line" lang="perl"></span>
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2177
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2316
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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="perl"><span class="sx" style="color: #d14;"> gene</span></span>
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2317
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<pre style="margin: 0;">+<span id="LC2317" class="line" lang="perl"><span class="sx" style="color: #d14;"> full_report Detailed Report</span></span>
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2178
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2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="perl"><span class="sx" style="color: #d14;"> gene_table Gene Table</span></span>
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2179
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2319
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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="perl"><span class="sx" style="color: #d14;"> native Gene Report</span></span>
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2180
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2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="perl"><span class="sx" style="color: #d14;"> native asn.1 Entrezgene ASN.1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2357,9 +2497,7 @@ sub xml_to_json {</td>
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2357
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2497
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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$conv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$xc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">XMLin</span><span class="p">(</span><span class="nv" style="color: teal;">$data</span><span class="p">);</span></span>
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2358
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2498
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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="perl"> <span class="nv" style="color: teal;">convert_bools</span><span class="p">(</span><span class="nv" style="color: teal;">$conv</span><span class="p">);</span></span>
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2359
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2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$jc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">JSON::</span><span class="nv" style="color: teal;">PP</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">ascii</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">pretty</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">allow_nonref</span><span class="p">;</span></span>
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2360
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<pre style="margin: 0;">-<span id="LC2360" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$jc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">encode</span><span class="p">(</span><span class="nv" style="color: teal;">$conv</span><span class="p">);</span></span>
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2361
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<pre style="margin: 0;">-<span id="LC2361" class="line" lang="perl"></span>
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2362
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<pre style="margin: 0;">-<span id="LC2362" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$result"</span><span class="p">;</span></span>
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2500
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<pre style="margin: 0;">+<span id="LC2500" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$jc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">encode</span><span class="p">(</span><span class="nv" style="color: teal;">$conv</span><span class="p">);</span></span>
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2363
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2501
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<pre style="margin: 0;"> <span id="LC2501" class="line" lang="perl"></span>
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2364
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2502
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<pre style="margin: 0;"> <span id="LC2502" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$data</span><span class="p">;</span></span>
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2365
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2503
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<pre style="margin: 0;"> <span id="LC2503" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2405,6 +2543,7 @@ sub eftch {</td>
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2405
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2543
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<pre style="margin: 0;"> <span id="LC2543" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
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2406
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2544
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<pre style="margin: 0;"> <span id="LC2544" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
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2407
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2545
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<pre style="margin: 0;"> <span id="LC2545" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
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2546
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<pre style="margin: 0;">+<span id="LC2546" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
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2408
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2547
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<pre style="margin: 0;"> <span id="LC2547" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2409
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<td class="diff-line-num new_line" data-linenumber="2548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2548
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<pre style="margin: 0;"> <span id="LC2548" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
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2410
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2549
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<pre style="margin: 0;"> <span id="LC2549" class="line" lang="perl"> <span class="s" style="color: #d14;">"raw"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$raw</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2456,6 +2595,10 @@ sub eftch {</td>
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2456
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2595
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<pre style="margin: 0;"> <span id="LC2595" class="line" lang="perl"> <span class="nv" style="color: teal;">$style</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"withparts"</span><span class="p">;</span></span>
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2457
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2596
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<pre style="margin: 0;"> <span id="LC2596" class="line" lang="perl"> <span class="p">}</span></span>
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2458
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2597
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<pre style="margin: 0;"> <span id="LC2597" class="line" lang="perl"></span>
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2598
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<pre style="margin: 0;">+<span id="LC2598" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"gbc"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$mode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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2599
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<pre style="margin: 0;">+<span id="LC2599" class="line" lang="perl"> <span class="nv" style="color: teal;">$mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"xml"</span><span class="p">;</span></span>
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2600
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<pre style="margin: 0;">+<span id="LC2600" class="line" lang="perl"> <span class="p">}</span></span>
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2601
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<pre style="margin: 0;">+<span id="LC2601" class="line" lang="perl"></span>
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2459
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2602
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<pre style="margin: 0;"> <span id="LC2602" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">t</span> <span class="bp" style="color: #999;">STDIN</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: teal;">@ARGV</span> <span class="p">)</span> <span class="p">{</span></span>
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2460
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2603
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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$db</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$id</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2461
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<td class="diff-line-num new_line" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2517,7 +2660,7 @@ sub eftch {</td>
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2517
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<td class="diff-line-num new_line" data-linenumber="2660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2660
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<pre style="margin: 0;"> <span id="LC2660" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"docsum"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$fnc</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-summary"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2518
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<td class="diff-line-num new_line" data-linenumber="2661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
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<td class="diff-line-num new_line" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="perl"> <span class="nv" style="color: teal;">esmry</span> <span class="p">(</span> <span class="nv" style="color: teal;">$dbase</span><span class="p">,</span> <span class="nv" style="color: teal;">$web</span><span class="p">,</span> <span class="nv" style="color: teal;">$key</span><span class="p">,</span> <span class="nv" style="color: teal;">$num</span><span class="p">,</span> <span class="nv" style="color: teal;">$id</span><span class="p">,</span> <span class="nv" style="color: teal;">$mode</span><span class="p">,</span> <span class="nv" style="color: teal;">$min</span><span class="p">,</span> <span class="nv" style="color: teal;">$max</span><span class="p">,</span> <span class="nv" style="color: teal;">$tool</span><span class="p">,</span> <span class="nv" style="color: teal;">$email</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2520
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<td class="diff-line-num new_line old" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2520" class="line" lang="perl"> <span class="nv" style="color: teal;">$silent</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$debug</span><span class="p">,</span> <span class="nv" style="color: teal;">$log</span><span class="p">,</span> <span class="nv" style="color: teal;">$http</span><span class="p">,</span> <span class="nv" style="color: teal;">$alias</span><span class="p">,</span> <span class="nv" style="color: teal;">$basx</span> <span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2663
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<pre style="margin: 0;">+<span id="LC2663" class="line" lang="perl"> <span class="nv" style="color: teal;">$silent</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$debug</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">internal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$</span>log</span><span class="p">,</span> <span class="nv" style="color: teal;">$http</span><span class="p">,</span> <span class="nv" style="color: teal;">$alias</span><span class="p">,</span> <span class="nv" style="color: teal;">$basx</span> <span class="p">);</span></span>
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2521
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2664
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<pre style="margin: 0;"> <span id="LC2664" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2522
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<td class="diff-line-num new_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2665
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<pre style="margin: 0;"> <span id="LC2665" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
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<td class="diff-line-num new_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2666
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<pre style="margin: 0;"> <span id="LC2666" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2683,10 +2826,11 @@ sub eftch {</td>
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2683
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<td class="diff-line-num new_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2826
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<pre style="margin: 0;"> <span id="LC2826" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2684
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<td class="diff-line-num new_line" data-linenumber="2827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2827
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<pre style="margin: 0;"> <span id="LC2827" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"db=$dbase&id=$id"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2685
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<td class="diff-line-num new_line" data-linenumber="2828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2828
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<pre style="margin: 0;"> <span id="LC2828" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2686
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<td class="diff-line-num new_line old" data-linenumber="2829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2686" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"gb"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2829
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<pre style="margin: 0;">+<span id="LC2829" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"gb"</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">or</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"gbc"</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">{</span></span>
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2687
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<td class="diff-line-num new_line" data-linenumber="2830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2830
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<pre style="margin: 0;"> <span id="LC2830" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"withparts"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"master"</span> <span class="p">)</span> <span class="p">{</span></span>
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2688
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<pre style="margin: 0;">-<span id="LC2688" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=<span class="idiff left right">gbwithparts</span>"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2831
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<pre style="margin: 0;">+<span id="LC2831" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=<span class="idiff left right">$type</span>"</span><span class="p">;</span></span>
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2689
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2832
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<pre style="margin: 0;"> <span id="LC2832" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&retmode=$mode"</span><span class="p">;</span></span>
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2833
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<pre style="margin: 0;">+<span id="LC2833" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&style=$style"</span><span class="p">;</span></span>
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2690
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2834
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<pre style="margin: 0;"> <span id="LC2834" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"conwithfeat"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"withfeat"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"contigwithfeat"</span> <span class="p">)</span> <span class="p">{</span></span>
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2691
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2835
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<pre style="margin: 0;"> <span id="LC2835" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=$type"</span><span class="p">;</span></span>
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2692
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2836
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<pre style="margin: 0;"> <span id="LC2836" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&retmode=$mode"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2826,10 +2970,11 @@ sub eftch {</td>
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2826
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2970
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<pre style="margin: 0;"> <span id="LC2970" class="line" lang="perl"></span>
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2827
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2971
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<pre style="margin: 0;"> <span id="LC2971" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"db=$dbase&query_key=$key&WebEnv=$web"</span><span class="p">;</span></span>
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2828
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2972
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<pre style="margin: 0;"> <span id="LC2972" class="line" lang="perl"></span>
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2829
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<pre style="margin: 0;">-<span id="LC2829" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"gb"</span> <span class="p">)</span> <span class="p">{</span></span>
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2973
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<pre style="margin: 0;">+<span id="LC2973" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"gb"</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">or</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"gbc"</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">{</span></span>
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2830
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2974
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<pre style="margin: 0;"> <span id="LC2974" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"withparts"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"master"</span> <span class="p">)</span> <span class="p">{</span></span>
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2831
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<pre style="margin: 0;">-<span id="LC2831" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=<span class="idiff left right">gbwithparts</span>"</span><span class="p">;</span></span>
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2975
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<pre style="margin: 0;">+<span id="LC2975" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=<span class="idiff left right">$type</span>"</span><span class="p">;</span></span>
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2832
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2976
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<pre style="margin: 0;"> <span id="LC2976" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&retmode=$mode"</span><span class="p">;</span></span>
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2977
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<pre style="margin: 0;">+<span id="LC2977" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&style=$style"</span><span class="p">;</span></span>
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2833
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2978
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<pre style="margin: 0;"> <span id="LC2978" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"conwithfeat"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"withfeat"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: teal;">$style</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"contigwithfeat"</span> <span class="p">)</span> <span class="p">{</span></span>
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2834
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2979
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<pre style="margin: 0;"> <span id="LC2979" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&rettype=$type"</span><span class="p">;</span></span>
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2835
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2980
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<pre style="margin: 0;"> <span id="LC2980" class="line" lang="perl"> <span class="nv" style="color: teal;">$arg</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"&retmode=$mode"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3034,6 +3179,7 @@ sub einfo {</td>
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3034
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<td class="diff-line-num new_line" data-linenumber="3179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3179
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3179" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3035
</td>
<td class="diff-line-num new_line" data-linenumber="3180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3180
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3180" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3036
</td>
<td class="diff-line-num new_line" data-linenumber="3181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3181
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3181" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3182
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3182" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3037
</td>
<td class="diff-line-num new_line" data-linenumber="3183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3183
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3183" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3038
</td>
<td class="diff-line-num new_line" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3184
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3184" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3039
</td>
<td class="diff-line-num new_line" data-linenumber="3185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3185
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3185" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3125,6 +3271,7 @@ sub einfo {</td>
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<td class="diff-line-num old_line" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3125
</td>
<td class="diff-line-num new_line" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3271
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3271" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3126
</td>
<td class="diff-line-num new_line" data-linenumber="3272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3272
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3272" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$output</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3127
</td>
<td class="diff-line-num new_line" data-linenumber="3273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3273
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3273" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Failure of '$url'\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3274
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3274" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3128
</td>
<td class="diff-line-num new_line" data-linenumber="3275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3275
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3275" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3129
</td>
<td class="diff-line-num new_line" data-linenumber="3276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3276
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3276" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3130
</td>
<td class="diff-line-num new_line" data-linenumber="3277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3277
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3277" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3575,6 +3722,7 @@ sub elink {</td>
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<td class="diff-line-num old_line" data-linenumber="3575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3575
</td>
<td class="diff-line-num new_line" data-linenumber="3722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3722
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3722" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3576
</td>
<td class="diff-line-num new_line" data-linenumber="3723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3723
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3723" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3577
</td>
<td class="diff-line-num new_line" data-linenumber="3724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3724
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3724" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3725
</td>
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<pre style="margin: 0;">+<span id="LC3725" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3578
</td>
<td class="diff-line-num new_line" data-linenumber="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3726
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3726" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3579
</td>
<td class="diff-line-num new_line" data-linenumber="3727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3727
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3727" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3580
</td>
<td class="diff-line-num new_line" data-linenumber="3728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3728
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3728" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3929,6 +4077,7 @@ sub entfy {</td>
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<td class="diff-line-num old_line" data-linenumber="3929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3929
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<td class="diff-line-num new_line" data-linenumber="4077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4077
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4077" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3930
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<td class="diff-line-num new_line" data-linenumber="4078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4078
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<pre style="margin: 0;"> <span id="LC4078" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3931
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<td class="diff-line-num new_line" data-linenumber="4079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4079
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<pre style="margin: 0;"> <span id="LC4079" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4080
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4080" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3932
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<td class="diff-line-num new_line" data-linenumber="4081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4081
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4081" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3933
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<td class="diff-line-num new_line" data-linenumber="4082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4082
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<pre style="margin: 0;"> <span id="LC4082" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3934
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<td class="diff-line-num new_line" data-linenumber="4083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4083
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<pre style="margin: 0;"> <span id="LC4083" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4102,6 +4251,7 @@ sub epost {</td>
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<td class="diff-line-num old_line" data-linenumber="4102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4102
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<td class="diff-line-num new_line" data-linenumber="4251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4251
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4251" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4103
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<td class="diff-line-num new_line" data-linenumber="4252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4252
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4252" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4104
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<td class="diff-line-num new_line" data-linenumber="4253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4253
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4253" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4254
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<pre style="margin: 0;">+<span id="LC4254" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4105
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<td class="diff-line-num new_line" data-linenumber="4255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4255
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4255" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4106
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<td class="diff-line-num new_line" data-linenumber="4256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4256
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4256" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4107
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<td class="diff-line-num new_line" data-linenumber="4257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4257
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4257" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4317,6 +4467,7 @@ sub epost {</td>
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<td class="diff-line-num old_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4317
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<td class="diff-line-num new_line" data-linenumber="4467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4467
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4467" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4318
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<td class="diff-line-num new_line" data-linenumber="4468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4468
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4468" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4319
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<td class="diff-line-num new_line" data-linenumber="4469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4469
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4469" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$combo</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4470
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<pre style="margin: 0;">+<span id="LC4470" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4320
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<td class="diff-line-num new_line" data-linenumber="4471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4471
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<pre style="margin: 0;"> <span id="LC4471" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Failure of post to find data to load\n"</span><span class="p">;</span></span>
</pre>
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4321
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<td class="diff-line-num new_line" data-linenumber="4472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4472
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<pre style="margin: 0;"> <span id="LC4472" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4322
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<td class="diff-line-num new_line" data-linenumber="4473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4473
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<pre style="margin: 0;"> <span id="LC4473" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4369,6 +4520,7 @@ sub espel {</td>
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<td class="diff-line-num old_line" data-linenumber="4369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4369
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<td class="diff-line-num new_line" data-linenumber="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4520
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<pre style="margin: 0;"> <span id="LC4520" class="line" lang="perl"> <span class="nv" style="color: teal;">$spell_help</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4370
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<td class="diff-line-num new_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4521
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<pre style="margin: 0;"> <span id="LC4521" class="line" lang="perl"> <span class="s" style="color: #d14;">"db=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$db</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4371
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<td class="diff-line-num new_line" data-linenumber="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4522
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<pre style="margin: 0;"> <span id="LC4522" class="line" lang="perl"> <span class="s" style="color: #d14;">"query=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4523
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<pre style="margin: 0;">+<span id="LC4523" class="line" lang="perl"> <span class="s" style="color: #d14;">"q=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4372
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<td class="diff-line-num new_line" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4524
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<pre style="margin: 0;"> <span id="LC4524" class="line" lang="perl"> <span class="s" style="color: #d14;">"api_key=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$api_key</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4373
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<td class="diff-line-num new_line" data-linenumber="4525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4525
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<pre style="margin: 0;"> <span id="LC4525" class="line" lang="perl"> <span class="s" style="color: #d14;">"email=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$emaddr</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4374
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<td class="diff-line-num new_line" data-linenumber="4526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4526
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<pre style="margin: 0;"> <span id="LC4526" class="line" lang="perl"> <span class="s" style="color: #d14;">"tool=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$tuul</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4376,6 +4528,7 @@ sub espel {</td>
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<td class="diff-line-num old_line" data-linenumber="4376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4376
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<td class="diff-line-num new_line" data-linenumber="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4528
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<pre style="margin: 0;"> <span id="LC4528" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4377
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<td class="diff-line-num new_line" data-linenumber="4529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4529
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<pre style="margin: 0;"> <span id="LC4529" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4378
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<td class="diff-line-num new_line" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4530
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<pre style="margin: 0;"> <span id="LC4530" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4531
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<pre style="margin: 0;">+<span id="LC4531" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4379
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<td class="diff-line-num new_line" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4532
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4532" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4380
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<td class="diff-line-num new_line" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4533
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<pre style="margin: 0;"> <span id="LC4533" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4381
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<td class="diff-line-num new_line" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4534
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<pre style="margin: 0;"> <span id="LC4534" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4472,6 +4625,7 @@ sub ecitmtch {</td>
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<td class="diff-line-num old_line" data-linenumber="4472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4472
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<td class="diff-line-num new_line" data-linenumber="4625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4625
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4625" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4473
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<td class="diff-line-num new_line" data-linenumber="4626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4626
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<pre style="margin: 0;"> <span id="LC4626" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4474
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<td class="diff-line-num new_line" data-linenumber="4627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4627
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<pre style="margin: 0;"> <span id="LC4627" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4628
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<pre style="margin: 0;">+<span id="LC4628" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4475
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<td class="diff-line-num new_line" data-linenumber="4629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4629
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<pre style="margin: 0;"> <span id="LC4629" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4476
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<td class="diff-line-num new_line" data-linenumber="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4630
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<pre style="margin: 0;"> <span id="LC4630" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4477
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<td class="diff-line-num new_line" data-linenumber="4631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4631
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<pre style="margin: 0;"> <span id="LC4631" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4586,6 +4740,7 @@ sub eprxy {</td>
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<td class="diff-line-num old_line" data-linenumber="4586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4586
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<td class="diff-line-num new_line" data-linenumber="4740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4740
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<pre style="margin: 0;"> <span id="LC4740" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4587
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<td class="diff-line-num new_line" data-linenumber="4741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4741
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<pre style="margin: 0;"> <span id="LC4741" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4588
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<td class="diff-line-num new_line" data-linenumber="4742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4742
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<pre style="margin: 0;"> <span id="LC4742" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4743
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<pre style="margin: 0;">+<span id="LC4743" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4589
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<td class="diff-line-num new_line" data-linenumber="4744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4744
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<pre style="margin: 0;"> <span id="LC4744" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4590
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<td class="diff-line-num new_line" data-linenumber="4745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4745
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<pre style="margin: 0;"> <span id="LC4745" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4591
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<td class="diff-line-num new_line" data-linenumber="4746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4746
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<pre style="margin: 0;"> <span id="LC4746" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4821,13 +4976,16 @@ sub esrch {</td>
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<td class="diff-line-num old_line" data-linenumber="4821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4821
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<td class="diff-line-num new_line" data-linenumber="4976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4976
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<pre style="margin: 0;"> <span id="LC4976" class="line" lang="perl"> <span class="nv" style="color: teal;">$srch_help</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4822
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<td class="diff-line-num new_line" data-linenumber="4977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4977
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<pre style="margin: 0;"> <span id="LC4977" class="line" lang="perl"> <span class="s" style="color: #d14;">"db=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$db</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4823
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<td class="diff-line-num new_line" data-linenumber="4978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4978
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<pre style="margin: 0;"> <span id="LC4978" class="line" lang="perl"> <span class="s" style="color: #d14;">"query=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4979
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<pre style="margin: 0;">+<span id="LC4979" class="line" lang="perl"> <span class="s" style="color: #d14;">"q=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$query</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4824
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<td class="diff-line-num new_line" data-linenumber="4980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4980
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<pre style="margin: 0;"> <span id="LC4980" class="line" lang="perl"> <span class="s" style="color: #d14;">"sort=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$sort</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4825
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<td class="diff-line-num new_line" data-linenumber="4981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4981
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<pre style="margin: 0;"> <span id="LC4981" class="line" lang="perl"> <span class="s" style="color: #d14;">"days=i"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$rldate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4826
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<td class="diff-line-num new_line" data-linenumber="4982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4982
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<pre style="margin: 0;"> <span id="LC4982" class="line" lang="perl"> <span class="s" style="color: #d14;">"mindate=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$mndate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4827
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<td class="diff-line-num new_line" data-linenumber="4983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4983
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<pre style="margin: 0;"> <span id="LC4983" class="line" lang="perl"> <span class="s" style="color: #d14;">"maxdate=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$mxdate</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4828
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<td class="diff-line-num new_line" data-linenumber="4984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4984
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<pre style="margin: 0;"> <span id="LC4984" class="line" lang="perl"> <span class="s" style="color: #d14;">"datetype=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$dttype</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4829
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<td class="diff-line-num new_line" data-linenumber="4985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4985
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<pre style="margin: 0;"> <span id="LC4985" class="line" lang="perl"> <span class="s" style="color: #d14;">"label=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$lbl</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4986
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<pre style="margin: 0;">+<span id="LC4986" class="line" lang="perl"> <span class="s" style="color: #d14;">"journal=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$journal</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4830
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<td class="diff-line-num new_line" data-linenumber="4987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4987
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<pre style="margin: 0;"> <span id="LC4987" class="line" lang="perl"> <span class="s" style="color: #d14;">"pub=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$pub</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4988
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<pre style="margin: 0;">+<span id="LC4988" class="line" lang="perl"> <span class="s" style="color: #d14;">"released=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$released</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4831
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<td class="diff-line-num new_line" data-linenumber="4989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4989
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<pre style="margin: 0;"> <span id="LC4989" class="line" lang="perl"> <span class="s" style="color: #d14;">"country=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$country</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4832
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<td class="diff-line-num new_line" data-linenumber="4990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4990
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<pre style="margin: 0;"> <span id="LC4990" class="line" lang="perl"> <span class="s" style="color: #d14;">"feature=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$feature</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4833
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<td class="diff-line-num new_line" data-linenumber="4991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4991
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<pre style="margin: 0;"> <span id="LC4991" class="line" lang="perl"> <span class="s" style="color: #d14;">"location=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$location</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4836,6 +4994,7 @@ sub esrch {</td>
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<td class="diff-line-num old_line" data-linenumber="4836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4836
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<td class="diff-line-num new_line" data-linenumber="4994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4994
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<pre style="margin: 0;"> <span id="LC4994" class="line" lang="perl"> <span class="s" style="color: #d14;">"source=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$source</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4837
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<td class="diff-line-num new_line" data-linenumber="4995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4995
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<pre style="margin: 0;"> <span id="LC4995" class="line" lang="perl"> <span class="s" style="color: #d14;">"status=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$status</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4838
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<td class="diff-line-num new_line" data-linenumber="4996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4996
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<pre style="margin: 0;"> <span id="LC4996" class="line" lang="perl"> <span class="s" style="color: #d14;">"type=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$gtype</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4997
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<pre style="margin: 0;">+<span id="LC4997" class="line" lang="perl"> <span class="s" style="color: #d14;">"class=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$class</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4839
</td>
<td class="diff-line-num new_line" data-linenumber="4998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4998
</td>
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<pre style="margin: 0;"> <span id="LC4998" class="line" lang="perl"> <span class="s" style="color: #d14;">"clean"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$clean</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4840
</td>
<td class="diff-line-num new_line" data-linenumber="4999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4999
</td>
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<pre style="margin: 0;"> <span id="LC4999" class="line" lang="perl"> <span class="s" style="color: #d14;">"field=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$field</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4841
</td>
<td class="diff-line-num new_line" data-linenumber="5000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5000
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<pre style="margin: 0;"> <span id="LC5000" class="line" lang="perl"> <span class="s" style="color: #d14;">"word"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$word</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4853,6 +5012,7 @@ sub esrch {</td>
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<td class="diff-line-num old_line" data-linenumber="4853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4853
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<td class="diff-line-num new_line" data-linenumber="5012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5012
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5012" class="line" lang="perl"> <span class="s" style="color: #d14;">"silent"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$silent</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4854
</td>
<td class="diff-line-num new_line" data-linenumber="5013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5013
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5013" class="line" lang="perl"> <span class="s" style="color: #d14;">"verbose"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4855
</td>
<td class="diff-line-num new_line" data-linenumber="5014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5014
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5014" class="line" lang="perl"> <span class="s" style="color: #d14;">"debug"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$debug</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="5015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5015
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<pre style="margin: 0;">+<span id="LC5015" class="line" lang="perl"> <span class="s" style="color: #d14;">"internal"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$internal</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4856
</td>
<td class="diff-line-num new_line" data-linenumber="5016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5016
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5016" class="line" lang="perl"> <span class="s" style="color: #d14;">"log"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$log</span><span class="p">,</span></span>
</pre>
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4857
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<td class="diff-line-num new_line" data-linenumber="5017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5017
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<pre style="margin: 0;"> <span id="LC5017" class="line" lang="perl"> <span class="s" style="color: #d14;">"compact"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$compact</span><span class="p">,</span></span>
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4858
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<td class="diff-line-num new_line" data-linenumber="5018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5018
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<pre style="margin: 0;"> <span id="LC5018" class="line" lang="perl"> <span class="s" style="color: #d14;">"http=s"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$http</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4899,7 +5059,7 @@ sub esrch {</td>
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4899
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5059
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<pre style="margin: 0;"> <span id="LC5059" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">binmode</span> <span class="bp" style="color: #999;">STDOUT</span><span class="p">,</span> <span class="s" style="color: #d14;">":utf8"</span><span class="p">;</span></span>
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4900
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<td class="diff-line-num new_line" data-linenumber="5060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5060
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<pre style="margin: 0;"> <span id="LC5060" class="line" lang="perl"></span>
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4901
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<td class="diff-line-num new_line" data-linenumber="5061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5061
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<pre style="margin: 0;"> <span id="LC5061" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># support all efilter shortcut flags in esearch (undocumented)</span></span>
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4902
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<td class="diff-line-num new_line old" data-linenumber="5062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4902" class="line" lang="perl"> <span class="nv" style="color: teal;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">process_extras</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span><span class="p">,</span> <span class="nv" style="color: teal;">$pub</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">country</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$feature</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$location</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$molecule</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$organism</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$source</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$status</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$gtype</span></span> <span class="p">);</span></span>
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5062
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<pre style="margin: 0;">+<span id="LC5062" class="line" lang="perl"> <span class="nv" style="color: teal;">$query</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">process_extras</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span><span class="p">,</span> <span class="nv" style="color: teal;">$pub</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">released</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$journal</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$country</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$feature</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$location</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$molecule</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$organism</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$source</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$status</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$gtype</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$class</span></span> <span class="p">);</span></span>
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4903
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<td class="diff-line-num new_line" data-linenumber="5063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5063
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<pre style="margin: 0;"> <span id="LC5063" class="line" lang="perl"></span>
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4904
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<td class="diff-line-num new_line" data-linenumber="5064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5064
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<pre style="margin: 0;"> <span id="LC5064" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$query</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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4905
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<td class="diff-line-num new_line" data-linenumber="5065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5065
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<pre style="margin: 0;"> <span id="LC5065" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Must supply -query search expression on command line\n"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5250,3 +5410,5 @@ if ( scalar @ARGV > 0 and $ARGV[0] eq "-version" ) {</td>
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5250
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5410
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<pre style="margin: 0;"> <span id="LC5410" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="p">(</span><span class="bp" style="color: #999;">STDIN</span><span class="p">);</span></span>
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5251
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<td class="diff-line-num new_line" data-linenumber="5411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5411
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<pre style="margin: 0;"> <span id="LC5411" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="p">(</span><span class="bp" style="color: #999;">STDOUT</span><span class="p">);</span></span>
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5252
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<td class="diff-line-num new_line" data-linenumber="5412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5412
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<pre style="margin: 0;"> <span id="LC5412" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span> <span class="p">(</span><span class="bp" style="color: #999;">STDERR</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5413
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<pre style="margin: 0;">+<span id="LC5413" class="line" lang="perl"></span>
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5414
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<pre style="margin: 0;">+<span id="LC5414" class="line" lang="perl"><span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: teal;">$result</span><span class="p">;</span></span></pre>
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<li id="6d992cfe40999b8275e4d7351563ea4a41dcec5c">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#6d992cfe40999b8275e4d7351563ea4a41dcec5c"><strong>index-pubmed</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@ if [ "$#" -gt 0 ]</td>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"> <span class="nv" style="color: teal;">MASTER</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span><span class="k" style="font-weight: 600;">)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">CONFIG</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">MASTER</span><span class="k" style="font-weight: 600;">}</span></span>
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24
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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25
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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26
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_PUBMED_MASTER</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +71,7 @@ do</td>
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70
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MASTER</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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72
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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"></span>
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73
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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="nb" style="color: #0086b3;">dir </span><span class="k" style="font-weight: 600;">in </span><span class="idiff left right">Current </span>Indexed Inverted Merged Pubmed</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="nb" style="color: #0086b3;">dir </span><span class="k" style="font-weight: 600;">in </span>Indexed Inverted Merged Pubmed</span>
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74
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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76
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,19 +109,9 @@ echo "$seconds seconds"</td>
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108
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"><span class="nv" style="color: teal;">REF</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$seconds</span></span>
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109
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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110
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="shell"></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="shell"><span class="nv" style="color: teal;">seconds_start</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Collecting PubMed Records"</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="shell">pm-current <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/Current"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MASTER</span><span class="s2" style="color: #d14;">/Archive"</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="shell"><span class="nv" style="color: teal;">seconds_end</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="shell"><span class="nv" style="color: teal;">seconds</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>seconds_end <span class="o" style="font-weight: 600;">-</span> seconds_start<span class="k" style="font-weight: 600;">))</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$seconds</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="shell"><span class="nv" style="color: teal;">COL</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$seconds</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell"></span>
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120
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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="shell"><span class="nv" style="color: teal;">seconds_start</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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121
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Indexing PubMed Records"</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/Current"</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="shell">pm-index <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/Indexed"</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell">pm-index <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MASTER</span><span class="s2" style="color: #d14;">/Archive"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$WORKING</span><span class="s2" style="color: #d14;">/Indexed"</span></span>
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124
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"><span class="nv" style="color: teal;">seconds_end</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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125
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"><span class="nv" style="color: teal;">seconds</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>seconds_end <span class="o" style="font-weight: 600;">-</span> seconds_start<span class="k" style="font-weight: 600;">))</span></span>
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126
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$seconds</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,7 +151,6 @@ echo ""</td>
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160
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"DWN </span><span class="nv" style="color: teal;">$DWN</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"POP </span><span class="nv" style="color: teal;">$POP</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"REF </span><span class="nv" style="color: teal;">$REF</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"COL </span><span class="nv" style="color: teal;">$COL</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"IDX </span><span class="nv" style="color: teal;">$IDX</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"INV </span><span class="nv" style="color: teal;">$INV</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"MRG </span><span class="nv" style="color: teal;">$MRG</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,3 +162,20 @@ fetch-pubmed -path "$MASTER/Archive" |</td>
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172
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="shell">xtract <span class="nt" style="color: navy;">-pattern</span> Author <span class="nt" style="color: navy;">-if</span> Affiliation <span class="nt" style="color: navy;">-contains</span> Medicine <span class="se" style="color: #d14;">\</span></span>
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173
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="shell"> <span class="nt" style="color: navy;">-pfx</span> <span class="s2" style="color: #d14;">"Archive and Index are "</span> <span class="nt" style="color: navy;">-element</span> Initials</span>
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174
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$CONFIG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span>bash_profile</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$HOME</span><span class="s2" style="color: #d14;">/.bashrc"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$HOME</span>/.<span class="nv" style="color: teal;">$target</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'bashrc'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$HOME</span><span class="s2" style="color: #d14;">/.</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span>bashrc</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"For convenience, please execute the following to save the archive path to a variable:"</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" echo </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">export EDIRECT_PUBMED_MASTER='</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CONFIG</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> >>"</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\$</span><span class="s2" style="color: #d14;">HOME/.</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">""</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#eee670f25204100a6fabcf3a1caf31b48e8e2c61"><strong>local-phrase-search</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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4
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"query"</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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6
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$# </span><span class="nt" style="color: navy;">-gt</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="nt" style="color: navy;">-h</span> <span class="p">|</span> <span class="nt" style="color: navy;">-help</span> <span class="p">|</span> <span class="nt" style="color: navy;">--help</span> <span class="p">)</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">help</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> break</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nt" style="color: navy;">-debug</span> <span class="p">)</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> <span class="nv" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> shift</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">-path</span> <span class="p">|</span> <span class="nt" style="color: navy;">-master</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"> <span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> shift</span></span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="p">;;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">-count</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"count"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"> <span class="nt" style="color: navy;">-counts</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"counts"</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="nt" style="color: navy;">-countr</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"countr"</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: navy;">-countp</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"countp"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"> <span class="nt" style="color: navy;">-query</span> <span class="p">|</span> <span class="nt" style="color: navy;">-phrase</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"query"</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nt" style="color: navy;">-search</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"search"</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"> <span class="nt" style="color: navy;">-exact</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"exact"</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"> <span class="p">;;</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"> <span class="nt" style="color: navy;">-mock</span> <span class="p">)</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"mock"</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"> <span class="p">;;</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"> <span class="nt" style="color: navy;">-mocks</span> <span class="p">)</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"mocks"</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"> <span class="p">;;</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"> <span class="nt" style="color: navy;">-mockx</span> <span class="p">)</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell"> <span class="nv" style="color: teal;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"mockx"</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"> <span class="p">;;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"> -<span class="k" style="font-weight: 600;">*</span> <span class="p">)</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$0</span><span class="s2" style="color: #d14;">: Unrecognized option </span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="shell"> <span class="p">;;</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span> <span class="p">)</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">break</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell"> <span class="p">;;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: teal;">$mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"help"</span> <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOF</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell"><span class="sh" style="color: #d14;">USAGE: </span><span class="nv" style="color: teal;">$0</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="shell"><span class="sh" style="color: #d14;"> [-path path_to_pubmed_master]</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"><span class="sh" style="color: #d14;"> -count | -counts | -search | -exact | [-query]</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="shell"><span class="sh" style="color: #d14;"> query arguments</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="shell"><span class="sh" style="color: #d14;">EXAMPLE: local-phrase-search -query catabolite repress* AND protease inhibit*</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="no" style="color: teal;">EOF</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="shell"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_PUBMED_MASTER</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path to postings files or set EDIRECT_PUBMED_MASTER environment variable"</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">MASTER</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_PUBMED_MASTER</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="shell"> <span class="nv" style="color: teal;">MASTER</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">MASTER</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell"> <span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$MASTER</span><span class="s2" style="color: #d14;">/Postings"</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">argument</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="shell"> <span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$argument</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span><span class="k" style="font-weight: 600;">)</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="shell"> <span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">target</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"> <span class="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span>/Postings <span class="p">)</span> <span class="p">;;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span> <span class="p">)</span> <span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$target</span>/Postings <span class="p">;;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"><span class="nv" style="color: teal;">osname</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span> <span class="nt" style="color: navy;">-s</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/_NT-.*$/_NT/; s/^MINGW[0-9]*/CYGWIN/'</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$osname</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"CYGWIN_NT"</span> <span class="nt" style="color: navy;">-a</span> <span class="nt" style="color: navy;">-x</span> /bin/cygpath <span class="o" style="font-weight: 600;">]</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>cygpath <span class="nt" style="color: navy;">-w</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">target</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$debug</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"mode: </span><span class="nv" style="color: teal;">$mode</span><span class="s2" style="color: #d14;">, path: '</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">', args: '</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">'"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="shell"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;">case</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$mode</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">in</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>count <span class="p">)</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-count</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> </span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="shell"> <span class="p">;;</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="shell"> counts <span class="p">)</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-counts</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> </span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="shell"> <span class="p">;;</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="shell"> countr <span class="p">)</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-countr</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> </span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="shell"> countp <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-countp</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span> </span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="shell"> query <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-query</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="shell"> <span class="p">;;</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="shell"> search <span class="p">)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-search</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="shell"> <span class="p">;;</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="shell"> exact <span class="p">)</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-exact</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="shell"> mock <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-mock</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="shell"> mocks <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-mocks</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="shell"> mockx <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-mockx</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$*</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span></pre>
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<li id="0aae011363caa6b0a509245f540cbd08b70f0d78">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#0aae011363caa6b0a509245f540cbd08b70f0d78"><strong>nquire</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ use File::Spec;</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># nquire version number</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">5</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">9</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">BEGIN</span></span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,10 +63,12 @@ BEGIN</td>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">lib</span> <span class="nv" style="color: teal;">$LibDir</span><span class="p">;</span></span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">JSON::</span><span class="nv" style="color: teal;">PP</span><span class="p">;</span></span>
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66
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">LWP::</span><span class="nv" style="color: teal;">UserAgent</span><span class="p">;</span></span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">POSIX</span><span class="p">;</span></span>
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68
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">URI::</span><span class="nv" style="color: teal;">Escape</span><span class="p">;</span></span>
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69
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Net::</span><span class="nv" style="color: teal;">FTP</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">XML::</span><span class="nv" style="color: teal;">Simple</span><span class="p">;</span></span>
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70
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"></span>
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71
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># definitions</span></span>
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72
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,6 +83,7 @@ sub clearflags {</td>
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81
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="perl"> <span class="nv" style="color: teal;">$alias</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="perl"> <span class="nv" style="color: teal;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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83
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="perl"> <span class="nv" style="color: teal;">$j2x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">false</span><span class="p">;</span></span>
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84
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="perl"> <span class="nv" style="color: teal;">$output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="perl"><span class="p">}</span></span>
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86
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -229,6 +232,33 @@ sub do_uri_escape {</td>
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229
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$rslt</span><span class="p">;</span></span>
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230
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="perl"><span class="p">}</span></span>
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231
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="perl"></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">convert_bools</span> <span class="p">{</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">unrecognized</span><span class="p">;</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="perl"></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">local</span> <span class="o" style="font-weight: 600;">*</span><span class="nv" style="color: teal;">_convert_bools</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sub </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ref_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">ref</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$ref_type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Nothing.</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$ref_type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'HASH'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="perl"> <span class="nv" style="color: teal;">_convert_bools</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">values</span><span class="p">(</span><span class="o" style="font-weight: 600;">%</span><span class="p">{</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">});</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$ref_type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'ARRAY'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="perl"> <span class="nv" style="color: teal;">_convert_bools</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">@</span><span class="p">{</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="perl"> <span class="nv" style="color: teal;">$ref_type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'JSON::PP::Boolean'</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$ref_type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'Types::Serialiser::Boolean'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="perl"> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="perl"> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">?</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="perl"> <span class="p">}</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="perl"> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$unrecognized</span><span class="p">{</span><span class="nv" style="color: teal;">$ref_type</span><span class="p">};</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="perl"> <span class="p">}</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="perl"> <span class="p">};</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">_convert_bools</span><span class="p">;</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"><span class="p">}</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"></span>
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232
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># nquire executes an external URL query from command line arguments</span></span>
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233
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="perl"></span>
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234
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$nquire_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qq{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -439,8 +469,103 @@ Federated Query</td>
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439
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl"><span class="sx" style="color: #d14;"> }" |</span></span>
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440
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern result -block binding -element "binding\@name" literal</span></span>
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441
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="perl"></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="perl"><span class="sx" style="color: #d14;">BioThings Queries</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="perl"></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -variant variant "chr6:g.26093141G>A" -fields dbsnp.gene |</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern gene -element \@geneid</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="perl"></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene query -q "symbol:OPN1MW" -species 9606 |</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern hits -element "\@_id"</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="perl"></span>
</pre>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene query -q "symbol:OPN1MW AND taxid:9606" |</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern hits -element "\@_id"</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="perl"></span>
</pre>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene gene 2652 -fields pathway.wikipathways |</span></span>
</pre>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern pathway -element "\@id"</span></span>
</pre>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="perl"></span>
</pre>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene query -q "pathway.wikipathways.id:WP455" -size 300 |</span></span>
</pre>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern hits -element "\@_id"</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="perl"></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -chem query -q "drugbank.targets.uniprot:P05231 AND drugbank.targets.actions:inhibitor" -fields hgvs |</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern hits -element "\@_id"</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="perl"></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="perl"><span class="sx" style="color: #d14;">EDirect Expansion</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="perl"></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="perl"><span class="sx" style="color: #d14;"> ExtractIDs() {</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -pattern BIO_THINGS -block Id -tab "\\n" -element "Id"</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="perl"><span class="sx" style="color: #d14;"> }</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="perl"></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="perl"><span class="sx" style="color: #d14;"> WrapIDs() {</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -wrp BIO_THINGS -pattern opt -wrp "Type" -lbl "\$1" \\</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="perl"><span class="sx" style="color: #d14;"> -wrp "Count" -num "\$2" -block "\$2" -wrp "Id" -element "\$3" |</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="perl"><span class="sx" style="color: #d14;"> xtract -format</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="perl"><span class="sx" style="color: #d14;"> }</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="perl"></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene query -q "symbol:OPN1MW AND taxid:9606" |</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="perl"><span class="sx" style="color: #d14;"> WrapIDs entrezgene hits "\@entrezgene" |</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="perl"></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="perl"><span class="sx" style="color: #d14;"> ExtractIDs |</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="perl"><span class="sx" style="color: #d14;"> while read geneid</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="perl"><span class="sx" style="color: #d14;"> do</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene gene "\$geneid" -fields pathway.wikipathways</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="perl"><span class="sx" style="color: #d14;"> done |</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="perl"><span class="sx" style="color: #d14;"> WrapIDs pathway.wikipathways.id pathway "\@id" |</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="perl"></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="perl"><span class="sx" style="color: #d14;"> ExtractIDs |</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="perl"><span class="sx" style="color: #d14;"> while read pathid</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="perl"><span class="sx" style="color: #d14;"> do</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="perl"><span class="sx" style="color: #d14;"> nquire -gene query -q "pathway.wikipathways.id:\$pathid" -size 300</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="perl"><span class="sx" style="color: #d14;"> done |</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="perl"><span class="sx" style="color: #d14;"> WrapIDs entrezgene hits "\@entrezgene" |</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="perl"></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="perl"><span class="sx" style="color: #d14;"> ExtractIDs |</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="perl"><span class="sx" style="color: #d14;"> sort -n</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="perl"></span>
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442
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="perl"><span class="sx" style="color: #d14;">}</span><span class="p">;</span></span>
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443
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="perl"></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@pubchem_properties</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw(</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="perl"><span class="sx" style="color: #d14;"> MolecularFormula</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="perl"><span class="sx" style="color: #d14;"> MolecularWeight</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="perl"><span class="sx" style="color: #d14;"> CanonicalSMILES</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="perl"><span class="sx" style="color: #d14;"> IsomericSMILES</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="perl"><span class="sx" style="color: #d14;"> InChI</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="perl"><span class="sx" style="color: #d14;"> InChIKey</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="perl"><span class="sx" style="color: #d14;"> IUPACName</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="perl"><span class="sx" style="color: #d14;"> XLogP</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="perl"><span class="sx" style="color: #d14;"> ExactMass</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="perl"><span class="sx" style="color: #d14;"> MonoisotopicMass</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="perl"><span class="sx" style="color: #d14;"> TPSA</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="perl"><span class="sx" style="color: #d14;"> Complexity</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="perl"><span class="sx" style="color: #d14;"> Charge</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="perl"><span class="sx" style="color: #d14;"> HBondDonorCount</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="perl"><span class="sx" style="color: #d14;"> HBondAcceptorCount</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="perl"><span class="sx" style="color: #d14;"> RotatableBondCount</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="perl"><span class="sx" style="color: #d14;"> HeavyAtomCount</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="perl"><span class="sx" style="color: #d14;"> IsotopeAtomCount</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="perl"><span class="sx" style="color: #d14;"> AtomStereoCount</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="perl"><span class="sx" style="color: #d14;"> DefinedAtomStereoCount</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="perl"><span class="sx" style="color: #d14;"> UndefinedAtomStereoCount</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="perl"><span class="sx" style="color: #d14;"> BondStereoCount</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="perl"><span class="sx" style="color: #d14;"> DefinedBondStereoCount</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="perl"><span class="sx" style="color: #d14;"> UndefinedBondStereoCount</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="perl"><span class="sx" style="color: #d14;"> CovalentUnitCount</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="perl"><span class="sx" style="color: #d14;"> Volume3D</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="perl"><span class="sx" style="color: #d14;"> XStericQuadrupole3D</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="perl"><span class="sx" style="color: #d14;"> YStericQuadrupole3D</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="perl"><span class="sx" style="color: #d14;"> ZStericQuadrupole3D</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureCount3D</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureAcceptorCount3D</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureDonorCount3D</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureAnionCount3D</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureCationCount3D</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureRingCount3D</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="perl"><span class="sx" style="color: #d14;"> FeatureHydrophobeCount3D</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="perl"><span class="sx" style="color: #d14;"> ConformerModelRMSD3D</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="perl"><span class="sx" style="color: #d14;"> EffectiveRotorCount3D</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="perl"><span class="sx" style="color: #d14;"> ConformerCount3D</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="perl"><span class="sx" style="color: #d14;"> Fingerprint2D</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="perl"><span class="sx" style="color: #d14;">)</span><span class="p">;</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="perl"></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">nquire</span> <span class="p">{</span></span>
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445
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="perl"></span>
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446
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># nquire -url http://... -tag value -tag value | ...</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -450,10 +575,19 @@ sub nquire {</td>
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450
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="perl"> <span class="nv" style="color: teal;">$pfx</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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451
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="perl"> <span class="nv" style="color: teal;">$amp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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452
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="perl"> <span class="nv" style="color: teal;">$pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="perl"> <span class="nv" style="color: teal;">$sfx</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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453
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="perl"></span>
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454
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="perl"> <span class="nv" style="color: teal;">@args</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@ARGV</span><span class="p">;</span></span>
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455
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="perl"> <span class="nv" style="color: teal;">$max</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: teal;">@args</span><span class="p">;</span></span>
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456
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="perl"></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="perl"> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">biothingsHash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="perl"> <span class="s" style="color: #d14;">'-gene'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'http://mygene.info/v3'</span><span class="p">,</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="perl"> <span class="s" style="color: #d14;">'-variant'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'http://myvariant.info/v1'</span><span class="p">,</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="perl"> <span class="s" style="color: #d14;">'-chem'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'http://mychem.info/v1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="perl"> <span class="s" style="color: #d14;">'-drug'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'http://c.biothings.io/v1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="perl"> <span class="s" style="color: #d14;">'-taxon'</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'http://t.biothings.io/v1'</span><span class="p">,</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="perl"> <span class="p">);</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="perl"></span>
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$max</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">{</span></span>
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458
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -515,12 +649,10 @@ sub nquire {</td>
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649
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="perl"> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">cwd</span><span class="p">(</span><span class="nv" style="color: teal;">$dir</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Unable to change to $dir: "</span><span class="p">,</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="sr" style="color: #009926;">message</span><span class="p">;</span></span>
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516
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="perl"> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">binary</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">warn</span> <span class="s" style="color: #d14;">"Unable to set binary mode: "</span><span class="p">,</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="sr" style="color: #009926;">message</span><span class="p">;</span></span>
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517
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651
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span> <span class="nv" style="color: teal;">$fl</span><span class="p">)</span> <span class="p">{</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">get</span><span class="p">(</span><span class="nv" style="color: teal;">$fl</span><span class="p">,</span> <span class="s" style="color: #d14;">"/dev/stdout"</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="sr" style="color: #009926;">message</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="nv" style="color: teal;">$msg</span><span class="p">;</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\nFAILED TO DOWNLOAD:\n\n$fl ($msg\n"</span><span class="p">;</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="perl"> <span class="p">}</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">get</span><span class="p">(</span><span class="nv" style="color: teal;">$fl</span><span class="p">,</span> <span class="s" style="color: #d14;">"/dev/stdout"</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ftp</span><span class="o" style="font-weight: 600;">-></span><span class="sr" style="color: #009926;">message</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span> <span class="nv" style="color: teal;">$msg</span><span class="p">;</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\nFAILED TO DOWNLOAD:\n\n$fl ($msg\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="perl"> <span class="p">}</span></span>
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -529,7 +661,7 @@ sub nquire {</td>
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="perl"> <span class="p">}</span></span>
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="perl"> <span class="p">}</span></span>
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if present, -http get or -get must be next</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if present, -http get or -get must be next<span class="idiff left right"> (now also allow -http post or -post)</span></span></span>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="perl"></span>
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># nquire -get -url "http://collections.mnh.si.edu/services/resolver/resolver.php" -voucher "Birds:625456"</span></span>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -544,6 +676,9 @@ sub nquire {</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-get"</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="perl"> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"get"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-post"</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="perl"> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"post"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="perl"> <span class="p">}</span></span>
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="perl"> <span class="p">}</span></span>
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -605,6 +740,13 @@ sub nquire {</td>
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605
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$max</span> <span class="p">)</span> <span class="p">{</span></span>
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606
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://eutilstest.ncbi.nlm.nih.gov/entrez/eutils"</span><span class="p">;</span></span>
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607
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="perl"> <span class="p">}</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-qa"</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># shortcut for eutils QA base (undocumented)</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$max</span> <span class="p">)</span> <span class="p">{</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://qa.ncbi.nlm.nih.gov/entrez/eutils"</span><span class="p">;</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="perl"> <span class="p">}</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="perl"></span>
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608
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-hydra"</span> <span class="p">)</span> <span class="p">{</span></span>
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609
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># internal citation match request (undocumented)</span></span>
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610
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -617,6 +759,7 @@ sub nquire {</td>
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617
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="perl"> <span class="nv" style="color: teal;">$amp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"&"</span><span class="p">;</span></span>
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618
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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619
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="perl"> <span class="p">}</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="perl"></span>
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620
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-revhist"</span> <span class="p">)</span> <span class="p">{</span></span>
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621
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># internal sequence revision history request (undocumented)</span></span>
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622
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -627,6 +770,47 @@ sub nquire {</td>
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627
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="perl"> <span class="nv" style="color: teal;">$amp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"&"</span><span class="p">;</span></span>
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628
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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629
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="perl"> <span class="p">}</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="perl"></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-pubchem"</span> <span class="p">)</span> <span class="p">{</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># shortcut for PubChem Power User Gateway REST service base (undocumented)</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># nquire -pubchem "compound/name/creatine/property" "IUPACName,MolecularWeight,MolecularFormula" "XML"</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$max</span> <span class="p">)</span> <span class="p">{</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://pubchem.ncbi.nlm.nih.gov/rest/pug"</span><span class="p">;</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: teal;">$max</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"compound"</span> <span class="p">)</span> <span class="p">{</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># even shorter shortcut</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># nquire -pubchem compound creatine</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="perl"> <span class="nv" style="color: teal;">$pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$args</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^-(.+)/</span> <span class="p">)</span> <span class="p">{</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/\//</span> <span class="p">)</span> <span class="p">{</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"/compound/name/"</span><span class="p">;</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="perl"> <span class="nv" style="color: teal;">$pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">map_macros ($pa</span><span class="nv" style="color: teal;">t</span><span class="p">);</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$pat</span><span class="p">;</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"/property/"</span><span class="p">;</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="perl"> <span class="nv" style="color: teal;">$sfx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="nv" style="color: teal;">@pubchem_properties</span><span class="p">);</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$sfx</span><span class="p">;</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"/XML"</span><span class="p">;</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="perl"> <span class="p">}</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="perl"> <span class="p">}</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="perl"></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$biothingsHash</span><span class="p">{</span><span class="nv" style="color: teal;">$pat</span><span class="p">}</span> <span class="p">)</span> <span class="p">{</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># shortcuts for biothings services (undocumented)</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$biothingsHash</span><span class="p">{</span><span class="nv" style="color: teal;">$pat</span><span class="p">};</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$http</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="perl"> <span class="nv" style="color: teal;">$http</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"get"</span><span class="p">;</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="perl"> <span class="p">}</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="perl"> <span class="nv" style="color: teal;">$j2x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">true</span><span class="p">;</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="perl"></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-wikipathways"</span> <span class="p">)</span> <span class="p">{</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># shortcut for webservice.wikipathways.org (undocumented)</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$max</span> <span class="p">)</span> <span class="p">{</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="perl"> <span class="nv" style="color: teal;">$url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://webservice.wikipathways.org"</span><span class="p">;</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="perl"> <span class="p">}</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="perl"></span>
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630
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span> <span class="nv" style="color: teal;">$pat</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-biosample"</span> <span class="p">)</span> <span class="p">{</span></span>
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631
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># internal biosample_chk request on live database (undocumented)</span></span>
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632
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="perl"> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -709,6 +893,33 @@ sub nquire {</td>
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709
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893
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># perform query</span></span>
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710
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="perl"> <span class="nv" style="color: teal;">$output</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">do_post</span> <span class="p">(</span><span class="nv" style="color: teal;">$url</span><span class="p">,</span> <span class="nv" style="color: teal;">$arg</span><span class="p">);</span></span>
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711
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="perl"></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$j2x</span> <span class="p">)</span> <span class="p">{</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$jc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">JSON::</span><span class="nv" style="color: teal;">PP</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">ascii</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">pretty</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">allow_nonref</span><span class="p">;</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$conv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$jc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">decode</span><span class="p">(</span><span class="nv" style="color: teal;">$output</span><span class="p">);</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="perl"> <span class="nv" style="color: teal;">convert_bools</span><span class="p">(</span><span class="nv" style="color: teal;">$conv</span><span class="p">);</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">XMLout</span><span class="p">(</span><span class="nv" style="color: teal;">$conv</span><span class="p">,</span> <span class="nv" style="color: teal;">SuppressEmpty</span> <span class="o" style="font-weight: 600;">=></span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">);</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="perl"></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove newlines, tabs, space between tokens, compress runs of spaces</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\r/ /g</span><span class="p">;</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\n/ /g</span><span class="p">;</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\t//g</span><span class="p">;</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ +/ /g</span><span class="p">;</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/> +</></g</span><span class="p">;</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="perl"></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove <opt> flanking object</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/<opt>\s*?</</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/>\s*?<\/opt>/</span> <span class="p">)</span> <span class="p">{</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/<opt>\s*?</</g</span><span class="p">;</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/>\s*?<\/opt>/>/g</span><span class="p">;</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="perl"> <span class="p">}</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="perl"> <span class="nv" style="color: teal;">$output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$result"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># restore newlines between objects</span></span>
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<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="perl"> <span class="nv" style="color: teal;">$output</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/> *?</>\n</g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="perl"></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">binmode</span><span class="p">(</span><span class="bp" style="color: #999;">STDOUT</span><span class="p">,</span> <span class="s" style="color: #d14;">":utf8"</span><span class="p">);</span></span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="perl"> <span class="p">}</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="perl"></span>
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712
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923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$output"</span><span class="p">;</span></span>
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713
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="perl"><span class="p">}</span></span>
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714
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="perl"></span>
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<li id="c352328f4ee63c03c5040ae93a0eb830264a05b8">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#c352328f4ee63c03c5040ae93a0eb830264a05b8"><strong>pm-clean</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path for cleaned files"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">target</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>fl <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.xml.gz</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">fl</span><span class="p">%.xml.gz</span><span class="k" style="font-weight: 600;">}</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span> <span class="o" style="font-weight: 600;">]</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> continue</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">"</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span> |</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-mixed</span> <span class="nt" style="color: navy;">-format</span> flush |</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<li id="cf42ceaa50c4e25d98dbe78f90643cc3e9d86e12">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#cf42ceaa50c4e25d98dbe78f90643cc3e9d86e12"><strong>pm-current</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path for current files"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">shift</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">target</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path for archive files"</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nv" style="color: teal;">archive</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">shift</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nv" style="color: teal;">archive</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">archive</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.xml.gz"</span> <span class="nt" style="color: navy;">-delete</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span>0</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="nv" style="color: teal;">chunk_size</span><span class="o" style="font-weight: 600;">=</span>250000</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_CHUNK_SIZE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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31
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">chunk_size</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_CHUNK_SIZE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>chunk_size <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span><span class="k" style="font-weight: 600;">))</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="nv" style="color: teal;">loop_max</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span><span class="m" style="color: #099;">50000000</span> <span class="o" style="font-weight: 600;">/</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">seq </span>1 <span class="k" style="font-weight: 600;">$((</span>loop_max<span class="k" style="font-weight: 600;">))</span> | <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read </span>n</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">printf </span>pubmed%03d <span class="nv" style="color: teal;">$n</span><span class="k" style="font-weight: 600;">)</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span> <span class="o" style="font-weight: 600;">]</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>fr <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"> <span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>to <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">continue</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;"> XML"</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds_start</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">seq</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"%0.f"</span> <span class="nv" style="color: teal;">$fr</span> <span class="nv" style="color: teal;">$to</span> | stream-pubmed <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$archive</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"> <span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>fr <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"> <span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>to <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds_end</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>seconds_end <span class="o" style="font-weight: 600;">-</span> seconds_start<span class="k" style="font-weight: 600;">))</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$seconds</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="nv" style="color: teal;">fsize</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: navy;">-c</span> <<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span><span class="k" style="font-weight: 600;">)</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fsize</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-le</span> 300 <span class="o" style="font-weight: 600;">]</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">sleep </span>1</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<li id="e64e3a5e86d494db79b78797cac8bd67e4cfed02">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#e64e3a5e86d494db79b78797cac8bd67e4cfed02"><strong>pm-erase</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path to archive files"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">target</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell">rchive <span class="nt" style="color: navy;">-trie</span> <span class="nt" style="color: navy;">-gzip</span> |</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read dir</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">"</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#11e69d8774031d4963ce336f99d8a3eb59178485"><strong>pm-index</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,35 +2,74 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$0</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path for archive files"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">archive</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">shift</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nv" style="color: teal;">archive</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">archive</span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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5
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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6
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path for indexed files"</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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9
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: teal;">indexed</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">shift</span></span>
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12
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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13
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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nv" style="color: teal;"><span class="idiff left">target</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff right">target</span></span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: teal;"><span class="idiff left">indexed</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff right">indexed</span></span><span class="p">%/</span><span class="k" style="font-weight: 600;">}</span></span>
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14
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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15
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<td class="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="idiff left">find </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$target</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-name</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"*.e2x.gz"</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-delete</span></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">cd</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: teal;"><span class="idiff">$archive</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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16
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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>fl <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.xml.gz</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$indexed</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.e2x.gz"</span> <span class="nt" style="color: navy;">-delete</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: teal;">q</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span>0</span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: teal;">chunk_size</span><span class="o" style="font-weight: 600;">=</span>250000</span>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_CHUNK_SIZE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">chunk_size</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">EDIRECT_CHUNK_SIZE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>chunk_size <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span><span class="k" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nv" style="color: teal;">loop_max</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span><span class="m" style="color: #099;">50000000</span> <span class="o" style="font-weight: 600;">/</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">seq </span>1 <span class="k" style="font-weight: 600;">$((</span>loop_max<span class="k" style="font-weight: 600;">))</span> | <span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">read </span>n</span>
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18
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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19
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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">fl</span><span class="p">%.xml.gz</span><span class="k" style="font-weight: 600;">}</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">"</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">printf </span>pubmed%03d <span class="nv" style="color: teal;">$n</span><span class="k" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$indexed</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>fr <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>to <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;"> XML"</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds_start</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">/meshtree.txt"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span> |</span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">seq</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"%0.f"</span> <span class="nv" style="color: teal;">$fr</span> <span class="nv" style="color: teal;">$to</span> |</span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> fetch-pubmed <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$archive</span><span class="s2" style="color: #d14;">"</span> |</span>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-transform</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$dir</span><span class="s2" style="color: #d14;">/meshtree.txt"</span> <span class="nt" style="color: navy;">-e2index</span> |</span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="diff-line-num new_line old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$<span class="idiff left right">target</span></span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$<span class="idiff left right">indexed</span></span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span></span>
</pre>
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27
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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span> |</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">seq</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"%0.f"</span> <span class="nv" style="color: teal;">$fr</span> <span class="nv" style="color: teal;">$to</span> |</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"> fetch-pubmed <span class="nt" style="color: navy;">-path</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$archive</span><span class="s2" style="color: #d14;">"</span> |</span>
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29
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-e2index</span> |</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$<span class="idiff left right">target</span></span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$<span class="idiff left right">indexed</span></span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span></span>
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31
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">fr</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>fr <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> <span class="nv" style="color: teal;">to</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>to <span class="o" style="font-weight: 600;">+</span> chunk_size<span class="k" style="font-weight: 600;">))</span></span>
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32
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds_end</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">date</span> <span class="s2" style="color: #d14;">"+%s"</span><span class="k" style="font-weight: 600;">)</span></span>
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33
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"> <span class="nv" style="color: teal;">seconds</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$((</span>seconds_end <span class="o" style="font-weight: 600;">-</span> seconds_start<span class="k" style="font-weight: 600;">))</span></span>
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34
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$seconds</span><span class="s2" style="color: #d14;"> seconds"</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"> <span class="nv" style="color: teal;">fsize</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: navy;">-c</span> < <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$indexed</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.e2x.gz"</span><span class="k" style="font-weight: 600;">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fsize</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-le</span> 300 <span class="o" style="font-weight: 600;">]</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml.gz"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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35
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">sleep </span>1</span>
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36
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#716c166996616604a07e7a503a4c0312789ae38d"><strong>pm-log</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">printAdditions<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"> <span class="nv" style="color: teal;">f</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"> <span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">f</span><span class="p">%.xml.gz</span><span class="k" style="font-weight: 600;">}</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$f</span><span class="s2" style="color: #d14;">"</span> |</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-strict</span> <span class="nt" style="color: navy;">-pattern</span> PubmedArticle <span class="se" style="color: #d14;">\</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="nt" style="color: navy;">-block</span> MedlineCitation/PMID <span class="nt" style="color: navy;">-lbl</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-sep</span> <span class="s2" style="color: #d14;">"."</span> <span class="se" style="color: #d14;">\</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="nt" style="color: navy;">-element</span> MedlineCitation/PMID,MedlineCitation/PMID@Version</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell">printDeletions<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> <span class="nv" style="color: teal;">f</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">f</span><span class="p">%.xml.gz</span><span class="k" style="font-weight: 600;">}</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$f</span><span class="s2" style="color: #d14;">"</span> |</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-strict</span> <span class="nt" style="color: navy;">-pattern</span> DeleteCitation <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">-block</span> PMID <span class="nt" style="color: navy;">-lbl</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-tab</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">D</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-sep</span> <span class="s2" style="color: #d14;">"."</span> <span class="nt" style="color: navy;">-element</span> <span class="s2" style="color: #d14;">"PMID,@Version"</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>fl <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.xml.gz</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>printAdditions <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> printDeletions <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span> <span class="o" style="font-weight: 600;">></span> transactions.txt</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#47558d902ced6a797a4391efeecb1a99cd82d894"><strong>pm-repack</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>fl <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.xml.gz</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nv" style="color: teal;">base</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">fl</span><span class="p">%.xml.gz</span><span class="k" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span> | xtract <span class="nt" style="color: navy;">-strict</span> <span class="nt" style="color: navy;">-compress</span> <span class="nt" style="color: navy;">-format</span> flush <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.tmp"</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-input</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.tmp"</span> <span class="nt" style="color: navy;">-pattern</span> PubmedArticle <span class="nt" style="color: navy;">-element</span> MedlineCitation/PMID <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.uid"</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> rchive <span class="nt" style="color: navy;">-input</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.tmp"</span> <span class="nt" style="color: navy;">-unique</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.uid"</span> <span class="nt" style="color: navy;">-index</span> MedlineCitation/PMID <span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="nt" style="color: navy;">-head</span> <span class="s2" style="color: #d14;">"<PubmedArticleSet>"</span> <span class="nt" style="color: navy;">-tail</span> <span class="s2" style="color: #d14;">"</PubmedArticleSet>"</span> <span class="nt" style="color: navy;">-pattern</span> PubmedArticle |</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-format</span> indent <span class="nt" style="color: navy;">-xml</span> <span class="s1" style="color: #d14;">'<?xml version="1.0" encoding="UTF-8"?>'</span> <span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> <span class="nt" style="color: navy;">-doctype</span> <span class="s1" style="color: #d14;">'<!DOCTYPE PubmedArticleSet SYSTEM "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_180601.dtd">'</span> <span class="o" style="font-weight: 600;">></span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.xml"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.tmp"</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$base</span><span class="s2" style="color: #d14;">.uid"</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.xml.gz</span></pre>
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<li id="386185b94119409d5ca96da9f7d8ec512015a779">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#386185b94119409d5ca96da9f7d8ec512015a779"><strong>pm-stash</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,8 @@ deleteCitations() {</td>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell">reportVersioned<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> <span class="nv" style="color: teal;">inp</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"> <span class="nv" style="color: teal;">pmidlist</span><span class="o" style="font-weight: 600;">=</span>.TO-REPORT</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-input</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$inp</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-pattern</span> PubmedArticle <span class="nt" style="color: navy;">-block</span> MedlineCitation/PMID <span class="nt" style="color: navy;">-if</span> <span class="s2" style="color: #d14;">"@Version"</span> <span class="nt" style="color: navy;">-gt</span> 1 <span class="nt" style="color: navy;">-element</span> <span class="s2" style="color: #d14;">"PMID"</span> |</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"> xtract <span class="nt" style="color: navy;">-input</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$inp</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-pattern</span> PubmedArticle <span class="se" style="color: #d14;">\</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"> <span class="nt" style="color: navy;">-block</span> MedlineCitation/PMID <span class="nt" style="color: navy;">-if</span> <span class="s2" style="color: #d14;">"@Version"</span> <span class="nt" style="color: navy;">-gt</span> 1 <span class="nt" style="color: navy;">-element</span> <span class="s2" style="color: #d14;">"PMID"</span> |</span>
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49
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-n</span> | <span class="nb" style="color: #0086b3;">uniq</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$pmidlist</span></span>
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50
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> <span class="nv" style="color: teal;">$pmidlist</span> <span class="o" style="font-weight: 600;">]</span></span>
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51
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<li id="11f18d3ab727247f23018b716384d2eef6c29bd8">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#11f18d3ab727247f23018b716384d2eef6c29bd8"><strong>pm-uids</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"$#"</span> <span class="nt" style="color: navy;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Must supply path to archive files"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">target</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">find <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$target</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.xml.gz"</span> |</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s,.*/\(.*\)\.xml\.gz,\1,'</span> |</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: navy;">-n</span> | <span class="nb" style="color: #0086b3;">uniq</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#c8ed09262181f940571b5bfc414297a7534c6d87"><strong>pm-verify</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>fl <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">*</span>.gz</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-c</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$fl</span><span class="s2" style="color: #d14;">"</span> | xtract <span class="nt" style="color: navy;">-mixed</span> <span class="nt" style="color: navy;">-verify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#bc3afcd0e5aadf4b16071e20877f44f4d2834572"><strong>rchive.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,7 +62,7 @@ import (</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// RCHIVE VERSION AND HELP MESSAGE TEXT</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="go"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">rchiveVersion</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">"10.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">rchiveVersion</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">"10.<span class="idiff left right">9</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">rchiveHelp</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="go"><span class="s" style="color: #d14;">Processing Flags</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5794,7 +5794,7 @@ func main() {</td>
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<pre style="margin: 0;"> <span id="LC5794" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">dbug</span><span class="x"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC5795" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC5796" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// drain results, but suppress normal output</span></span>
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<pre style="margin: 0;">-<span id="LC5797" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">_</span></span><span class="x"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="x"><span class="idiff right"> </span></span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">unsq</span><span class="x"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC5797" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">unsq</span><span class="x"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC5798" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">recordCount</span><span class="o" style="font-weight: 600;">++</span></span>
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<pre style="margin: 0;"> <span id="LC5799" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Gosched</span><span class="p">()</span></span>
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5800
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5800
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<pre style="margin: 0;"> <span id="LC5800" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5922,7 +5922,7 @@ func main() {</td>
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5922
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5922
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<pre style="margin: 0;"> <span id="LC5922" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">dbug</span><span class="x"> </span><span class="p">{</span></span>
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5923
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5923
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<pre style="margin: 0;"> <span id="LC5923" class="line" lang="go"></span>
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5924
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5924
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<pre style="margin: 0;"> <span id="LC5924" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// drain results, but suppress normal output</span></span>
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5925
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<pre style="margin: 0;">-<span id="LC5925" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">_</span></span><span class="x"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="x"><span class="idiff right"> </span></span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">sptr</span><span class="x"> </span><span class="p">{</span></span>
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5925
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<pre style="margin: 0;">+<span id="LC5925" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">sptr</span><span class="x"> </span><span class="p">{</span></span>
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5926
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5926
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<pre style="margin: 0;"> <span id="LC5926" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">recordCount</span><span class="o" style="font-weight: 600;">++</span></span>
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5927
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5927
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<pre style="margin: 0;"> <span id="LC5927" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Gosched</span><span class="p">()</span></span>
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5928
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5928
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<pre style="margin: 0;"> <span id="LC5928" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6503,7 +6503,7 @@ func main() {</td>
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6503
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6503
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<pre style="margin: 0;"> <span id="LC6503" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">dbug</span><span class="x"> </span><span class="p">{</span></span>
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6504
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6504
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<pre style="margin: 0;"> <span id="LC6504" class="line" lang="go"></span>
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6505
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6505
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<pre style="margin: 0;"> <span id="LC6505" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// drain results, but suppress normal output</span></span>
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6506
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<pre style="margin: 0;">-<span id="LC6506" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">_</span></span><span class="x"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="x"><span class="idiff right"> </span></span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">rslq</span><span class="x"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6506" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">rslq</span><span class="x"> </span><span class="p">{</span></span>
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6507
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6507
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<pre style="margin: 0;"> <span id="LC6507" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">recordCount</span><span class="o" style="font-weight: 600;">++</span></span>
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6508
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6508
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<pre style="margin: 0;"> <span id="LC6508" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Gosched</span><span class="p">()</span></span>
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6509
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6509
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<pre style="margin: 0;"> <span id="LC6509" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#90381f4e965b1aea947ce9f0d8cccfdbe4d1d611"><strong>setup-deps.pl</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ my @lwp_deps = qw(Encode::Locale File::Listing</td>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"><span class="sx" style="color: #d14;"> HTTP:Cookies HTTP::Date HTTP::Message HTTP::Negotiate</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"><span class="sx" style="color: #d14;"> IO::Socket::SSL LWP::MediaTypes LWP::Protocol::https</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"><span class="sx" style="color: #d14;"> Net::HTTP URI WWW::RobotRules Mozilla::CA)</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$module</span> <span class="p">(</span><span class="nv" style="color: teal;">@lwp_deps</span><span class="p">,</span> <span class="s" style="color: #d14;">'Time::HiRes'</span><span class="p">,</span> <span class="s" style="color: #d14;">'JSON::PP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'XML::Simple'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl"><span class="k" style="font-weight: 600;">for</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$module</span> <span class="p">(</span><span class="nv" style="color: teal;">@lwp_deps</span><span class="p">,</span> <span class="s" style="color: #d14;">'Time::HiRes'</span><span class="p">,</span> <span class="s" style="color: #d14;">'JSON::PP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<span class="idiff left">MIME::Base64'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>XML::Simple'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">CheckAvailability</span><span class="p">(</span><span class="nv" style="color: teal;">$module</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"> <span class="nn" style="color: #555;">CPAN::</span><span class="nv" style="color: teal;">Shell</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">install</span><span class="p">(</span><span class="nv" style="color: teal;">$module</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="perl"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#a1f9c9e5796fffc51dc6a65b98226224c5841aca"><strong>test-pubmed-index</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ do</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ttl</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$uid</span><span class="s2" style="color: #d14;"> TRIM"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$uid</span><span class="s2" style="color: #d14;"> TRIM<span class="idiff left"> -- </span></span><span class="nv" style="color: teal;"><span class="idiff right">$ttl</span></span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">res</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>phrase-search <span class="nt" style="color: navy;">-exact</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ttl</span><span class="s2" style="color: #d14;">"</span><span class="sb" style="color: #d14;">`</span></span>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#f3da8dd1a5c431b81c7fe5222e4dfa4856aa8d01"><strong>transmute</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ use File::Spec;</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># transmute version number</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">5</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"10.<span class="idiff left right">9</span>"</span><span class="p">;</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="k" style="font-weight: 600;">BEGIN</span></span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +64,7 @@ BEGIN</td>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">lib</span> <span class="nv" style="color: teal;">$LibDir</span><span class="p">;</span></span>
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65
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"></span>
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66
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">JSON::</span><span class="nv" style="color: teal;">PP</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">MIME::</span><span class="nv" style="color: teal;">Base64</span><span class="p">;</span></span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">URI::</span><span class="nv" style="color: teal;">Escape</span><span class="p">;</span></span>
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68
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">XML::</span><span class="nv" style="color: teal;">Simple</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +103,11 @@ Transformation Commands</td>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"><span class="sx" style="color: #d14;">}</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Must supply -decode, -encode, -j2x, or -x2j on command line\n"</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># read required function argument</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Must supply conversion type on command line\n"</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># read optional parent object name</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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106
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="perl"></span>
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107
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">transmute</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,7 +136,7 @@ sub transmute {</td>
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131
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># perform specific conversions</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="perl"></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"<span class="idiff left">decode"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-decod</span>e"</span> <span class="p">)</span> <span class="p">{</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"<span class="idiff left">unescape"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-unescap</span>e"</span> <span class="p">)</span> <span class="p">{</span></span>
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135
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl"></span>
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136
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">uri_unescape</span><span class="p">(</span><span class="nv" style="color: teal;">$data</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,7 +149,7 @@ sub transmute {</td>
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144
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data"</span><span class="p">;</span></span>
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145
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="perl"> <span class="p">}</span></span>
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146
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="perl"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"e<span class="idiff left">ncode"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-encod</span>e"</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"e<span class="idiff left">scape"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$type</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"-escap</span>e"</span> <span class="p">)</span> <span class="p">{</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl"></span>
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149
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># compress runs of spaces</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ +/ /g</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,6 +159,20 @@ sub transmute {</td>
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154
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data"</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="perl"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"decode64"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-decode64"</span> <span class="p">)</span> <span class="p">{</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="perl"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">decode_base64</span><span class="p">(</span><span class="nv" style="color: teal;">$data</span><span class="p">);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data"</span><span class="p">;</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"> <span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"encode64"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-encode64"</span> <span class="p">)</span> <span class="p">{</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">encode_base64</span><span class="p">(</span><span class="nv" style="color: teal;">$data</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="perl"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data"</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="perl"></span>
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157
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"plain"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-plain"</span> <span class="p">)</span> <span class="p">{</span></span>
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158
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="perl"></span>
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159
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove embedded mixed-content tags</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -262,6 +281,96 @@ sub transmute {</td>
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262
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data\n"</span><span class="p">;</span></span>
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263
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="perl"> <span class="p">}</span></span>
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264
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"docsum"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-docsum"</span> <span class="p">)</span> <span class="p">{</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove newlines, tabs, space between tokens, compress runs of spaces</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\r/ /g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\n/ /g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\t//g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ +/ /g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/> +</></g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># move UID from attribute to object</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/<Id>\d+<\/Id>/i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/<DocumentSummary uid=\"(\d+)\">/<DocumentSummary><Id>$1<\/Id>/g</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"> <span class="p">}</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/<DocumentSummary uid=\"\d+\">/<DocumentSummary>/g</span><span class="p">;</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="perl"></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># fix bad encoding</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@accum</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@working</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$docsumset_attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/(.+?)<DocumentSummarySet(\s+.+?)?>(.+)<\/DocumentSummarySet>(.+)/s</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl"> <span class="nv" style="color: teal;">$prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl"> <span class="nv" style="color: teal;">$docsumset_attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$2</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$docset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$3</span><span class="p">;</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl"> <span class="nv" style="color: teal;">$suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$4</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$docset</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/<DocumentSummary>(.+?)<\/DocumentSummary>/sg</span><span class="p">);</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="nv" style="color: teal;">$val</span> <span class="p">(</span><span class="nv" style="color: teal;">@vals</span><span class="p">)</span> <span class="p">{</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="s" style="color: #d14;">"<DocumentSummary>"</span><span class="p">);</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/<Title>(.+?)<\/Title>/</span> <span class="p">)</span> <span class="p">{</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\&\;/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\<\;/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\>\;/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\</</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\>/</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\&\;/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\<\;/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\>\;/</span> <span class="p">)</span> <span class="p">{</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"> <span class="nn" style="color: #555;">HTML::Entities::</span><span class="nv" style="color: teal;">decode_entities</span><span class="p">(</span><span class="nv" style="color: teal;">$x</span><span class="p">);</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> <span class="p">}</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># removed mixed content tags</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">b</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">i</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">u</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">sup</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">sub</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|</</span><span class="nv" style="color: teal;">b</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|</</span><span class="nv" style="color: teal;">i</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|</</span><span class="nv" style="color: teal;">u</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|</</span><span class="nv" style="color: teal;">sup</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|</</span><span class="nv" style="color: teal;">sub</span><span class="o" style="font-weight: 600;">>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">b</span><span class="o" style="font-weight: 600;">/>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">i</span><span class="o" style="font-weight: 600;">/>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">u</span><span class="o" style="font-weight: 600;">/>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">sup</span><span class="o" style="font-weight: 600;">/>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="nv" style="color: teal;">s</span><span class="o" style="font-weight: 600;">|<</span><span class="nv" style="color: teal;">sub</span><span class="o" style="font-weight: 600;">/>||</span><span class="nv" style="color: teal;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Reencode any resulting less-than or greater-than entities to avoid breaking the XML.</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/</</g</span><span class="p">;</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/>/>/g</span><span class="p">;</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/<Title>(.+?)<\/Title>/<Title>$x<\/Title>/</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="perl"> <span class="p">}</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="p">}</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/<Summary>(.+?)<\/Summary>/</span> <span class="p">)</span> <span class="p">{</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\&\;/</span> <span class="p">)</span> <span class="p">{</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="perl"> <span class="nn" style="color: #555;">HTML::Entities::</span><span class="nv" style="color: teal;">decode_entities</span><span class="p">(</span><span class="nv" style="color: teal;">$x</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Reencode any resulting less-than or greater-than entities to avoid breaking the XML.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/</</g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="perl"> <span class="nv" style="color: teal;">$x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/>/>/g</span><span class="p">;</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="perl"> <span class="nv" style="color: teal;">$val</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/<Summary>(.+?)<\/Summary>/<Summary>$x<\/Summary>/</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl"> <span class="p">}</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="nv" style="color: teal;">$val</span> <span class="p">);</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@working</span><span class="p">,</span> <span class="s" style="color: #d14;">"</DocumentSummary>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="perl"> <span class="p">}</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="perl"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: teal;">@working</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@accum</span><span class="p">,</span> <span class="nv" style="color: teal;">$prefix</span><span class="p">);</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@accum</span><span class="p">,</span> <span class="s" style="color: #d14;">"<DocumentSummarySet$docsumset_attrs>"</span><span class="p">);</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@accum</span><span class="p">,</span> <span class="nv" style="color: teal;">@working</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@accum</span><span class="p">,</span> <span class="s" style="color: #d14;">"</DocumentSummarySet>"</span><span class="p">);</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="p">(</span><span class="nv" style="color: teal;">@accum</span><span class="p">,</span> <span class="nv" style="color: teal;">$suffix</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span> <span class="p">(</span><span class="s" style="color: #d14;">"\n"</span><span class="p">,</span> <span class="nv" style="color: teal;">@accum</span><span class="p">);</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\n\n/\n/g</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl"> <span class="p">}</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># restore newlines between objects</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="perl"> <span class="nv" style="color: teal;">$data</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/> *?</>\n</g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$data\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"json2xml"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-json2xml"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"j2x"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$type</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"-j2x"</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># convert JSON to XML</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -284,9 +393,6 @@ sub transmute {</td>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="perl"> <span class="nv" style="color: teal;">$result</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/>\s*?<\/opt>/>/g</span><span class="p">;</span></span>
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285
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="perl"> <span class="p">}</span></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># read optional parent object name</span></span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$obj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="perl"></span>
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290
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$obj</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$obj</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">""</span> <span class="p">)</span> <span class="p">{</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="perl"></span>
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292
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$xml</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<?xml version="1.0" encoding="UTF-8"?>'</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/compare/0ad84a2b84b29a5b58bbc04eac8d19cda6213f1a...1c42e99e91bbfb976d95038ed72113cc6d224482#96f5584f0d6dcaca2b56481ad25dbd045758ed30"><strong>xtract.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,7 +53,7 @@ import (</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// XTRACT VERSION AND HELP MESSAGE TEXT</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="go"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">xtractVersion</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">"10.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">xtractVersion</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">"10.<span class="idiff left right">9</span>"</span></span>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="go"></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span><span class="x"> </span><span class="n" style="color: #333;">xtractHelp</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">`</span></span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="go"><span class="s" style="color: #d14;">Overview</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,6 +202,7 @@ Text Processing</td>
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202
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="go"><span class="s" style="color: #d14;"> -terms Partition text at spaces</span></span>
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203
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="go"><span class="s" style="color: #d14;"> -words Split at punctuation marks</span></span>
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204
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="go"><span class="s" style="color: #d14;"> -pairs Adjacent informative words</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="go"><span class="s" style="color: #d14;"> -reverse Reverse words in string</span></span>
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205
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="go"><span class="s" style="color: #d14;"> -letters Separate individual letters</span></span>
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206
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="go"><span class="s" style="color: #d14;"> -clauses Break at phrase separators</span></span>
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207
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="go"><span class="s" style="color: #d14;"> -indices Index normalized words</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,6 +210,7 @@ Text Processing</td>
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209
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="go"><span class="s" style="color: #d14;">Sequence Processing</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="go"><span class="s" style="color: #d14;"> -revcomp Reverse-complement nucleotide sequence</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="go"><span class="s" style="color: #d14;"> -nucleic Subrange determines forward or revcomp</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="go"><span class="s" style="color: #d14;">Sequence Coordinates</span></span>
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214
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="go"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -270,7 +272,7 @@ Notes</td>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="go"></span>
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271
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="go"><span class="s" style="color: #d14;"> -num and -len selections are synonyms for Object Count (#) and Item Length (%).</span></span>
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272
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="go"></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="go"><span class="s" style="color: #d14;"> -words, -pairs, and -indices convert to lower case.</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="go"><span class="s" style="color: #d14;"> -words, -pairs, <span class="idiff left right">-reverse, </span>and -indices convert to lower case.</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="go"><span class="s" style="color: #d14;">Examples</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -457,10 +459,11 @@ Formatted Authors</td>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="go"><span class="s" style="color: #d14;"> xtract -pattern PubmedArticle -element MedlineCitation/PMID \</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="go"><span class="s" style="color: #d14;"> -block PubDate -sep "-" -element Year,Month,MedlineDate \</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="go"><span class="s" style="color: #d14;"> -block Author -sep " " -tab "" \</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="go"><span class="s" style="color: #d14;"> -element "&COM" Initials,LastName -COM "(, )"</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="go"><span class="s" style="color: #d14;"> -element "&COM" Initials,LastName -COM "(|)" |</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="go"><span class="s" style="color: #d14;"> perl -pe 's/(\t[^\t|]*)\|([^\t|]*)$/$1 and $2/; s/\|([^|]*)$/, and $1/; s/\|/, /g'</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="go"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="go"><span class="s" style="color: #d14;"> 1413997 1992-Oct RK Mortimer, CR Contopoulou, JS King</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="go"><span class="s" style="color: #d14;"> 6301692 1983-Apr MA Krasnow<span class="idiff left right">,</span> NR Cozzarelli</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="go"><span class="s" style="color: #d14;"> 1413997 1992-Oct RK Mortimer, CR Contopoulou, <span class="idiff left right">and </span>JS King</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="go"><span class="s" style="color: #d14;"> 6301692 1983-Apr MA Krasnow<span class="idiff left right"> and</span> NR Cozzarelli</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="go"><span class="s" style="color: #d14;"> 781293 1976-Jul MJ Casadaban</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="go"><span class="s" style="color: #d14;">Medical Subject Headings</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1640,6 +1643,7 @@ const (</td>
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">TERMS</span></span>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">WORDS</span></span>
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span></span>
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<pre style="margin: 0;">+<span id="LC1646" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">REVERSE</span></span>
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span></span>
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span></span>
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1645
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<td class="diff-line-num new_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1649
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">INDICES</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1697,6 +1701,7 @@ const (</td>
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<td class="diff-line-num old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1697
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<td class="diff-line-num new_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span></span>
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<td class="diff-line-num old_line" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1698
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<td class="diff-line-num new_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1702
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<pre style="margin: 0;"> <span id="LC1702" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span></span>
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<td class="diff-line-num old_line" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1699
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<td class="diff-line-num new_line" data-linenumber="1703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">NUCLEIC</span></span>
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1700
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<td class="diff-line-num new_line" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1705
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ELSE</span></span>
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<td class="diff-line-num old_line" data-linenumber="1701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1701
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<td class="diff-line-num new_line" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1706
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1706" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">VARIABLE</span></span>
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<td class="diff-line-num old_line" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1702
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<td class="diff-line-num new_line" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">VALUE</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1794,6 +1799,7 @@ var argTypeIs = map[string]ArgumentType{</td>
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<td class="diff-line-num old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1794
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<td class="diff-line-num new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-terms"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1795
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<td class="diff-line-num new_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-words"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1796
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<td class="diff-line-num new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-pairs"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1802
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<pre style="margin: 0;">+<span id="LC1802" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-reverse"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1797
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<td class="diff-line-num new_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-letters"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1798
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<td class="diff-line-num new_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-clauses"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1799
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<td class="diff-line-num new_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1805
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1805" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-indices"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1823,6 +1829,7 @@ var argTypeIs = map[string]ArgumentType{</td>
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<td class="diff-line-num old_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1823
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<td class="diff-line-num new_line" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1829
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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-bed-based"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1824
</td>
<td class="diff-line-num new_line" data-linenumber="1830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1830
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-bed-coords"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1825
</td>
<td class="diff-line-num new_line" data-linenumber="1831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1831
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1831" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-revcomp"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1832
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<pre style="margin: 0;">+<span id="LC1832" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-nucleic"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1826
</td>
<td class="diff-line-num new_line" data-linenumber="1833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1833
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1833" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-else"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">EXTRACTION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1827
</td>
<td class="diff-line-num new_line" data-linenumber="1834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1834
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1834" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-pfx"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">CUSTOMIZATION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1828
</td>
<td class="diff-line-num new_line" data-linenumber="1835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1835
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1835" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-sfx"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">CUSTOMIZATION</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1854,6 +1861,7 @@ var opTypeIs = map[string]OpType{</td>
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<td class="diff-line-num old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1854
</td>
<td class="diff-line-num new_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1861
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1861" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-terms"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1855
</td>
<td class="diff-line-num new_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1862
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1862" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-words"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1856
</td>
<td class="diff-line-num new_line" data-linenumber="1863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1863
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1863" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-pairs"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1864
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1864" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-reverse"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">REVERSE</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1857
</td>
<td class="diff-line-num new_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1865
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1865" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-letters"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1858
</td>
<td class="diff-line-num new_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1866
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1866" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-clauses"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1859
</td>
<td class="diff-line-num new_line" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1867
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1867" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-indices"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1917,6 +1925,7 @@ var opTypeIs = map[string]OpType{</td>
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<td class="diff-line-num old_line" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1917
</td>
<td class="diff-line-num new_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1925
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1925" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-bed-based"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1918
</td>
<td class="diff-line-num new_line" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1926
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1926" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-bed-coords"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1919
</td>
<td class="diff-line-num new_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1927
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1927" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-revcomp"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1928
</td>
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-nucleic"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">NUCLEIC</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1920
</td>
<td class="diff-line-num new_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1929
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1929" class="line" lang="go"><span class="x"> </span><span class="s" style="color: #d14;">"-else"</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">ELSE</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1921
</td>
<td class="diff-line-num new_line" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1930
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1930" class="line" lang="go"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1922
</td>
<td class="diff-line-num new_line" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="go"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2692,8 +2701,8 @@ func ParseArguments(cmdargs []string, pttrn string) *Block {</td>
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<td class="diff-line-num old_line" data-linenumber="2692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2692
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<td class="diff-line-num new_line" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2701
</td>
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<pre style="margin: 0;"> <span id="LC2701" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Operation</span><span class="p">{</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2693
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<td class="diff-line-num new_line" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2702
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2702" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">comm</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">comm</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2694
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<td class="diff-line-num new_line" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2703
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<pre style="margin: 0;"> <span id="LC2703" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">UNSET</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2695
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<td class="diff-line-num new_line old" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2695" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2696
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<td class="diff-line-num new_line old" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2696" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2704
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<pre style="margin: 0;">+<span id="LC2704" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">REVERSE</span></span><span class="p"><span class="idiff">,</span></span><span class="x"><span class="idiff right"> </span></span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2705
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2705" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">NUCLEIC</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="2697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2697
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<td class="diff-line-num new_line" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2706
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2706" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">TAB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">RET</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PFX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SFX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SEP</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LBL</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PFC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEQ</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PLG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ELG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WRP</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEF</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">COLOR</span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2698
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<td class="diff-line-num new_line" data-linenumber="2707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2707
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2707" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">UNSET</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2699
</td>
<td class="diff-line-num new_line" data-linenumber="2708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2708
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2708" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fprintf</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stderr</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: No -element before '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2872,8 +2881,8 @@ func ParseArguments(cmdargs []string, pttrn string) *Block {</td>
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<td class="diff-line-num old_line" data-linenumber="2872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2872
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<td class="diff-line-num new_line" data-linenumber="2881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2881
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2881" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">switch</span><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2873
</td>
<td class="diff-line-num new_line" data-linenumber="2882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2882
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2882" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">UNSET</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="2874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2874
</td>
<td class="diff-line-num new_line" data-linenumber="2883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2883
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2883" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">nextStatus</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2875
</td>
<td class="diff-line-num new_line old" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2875" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
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2876
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<pre style="margin: 0;">-<span id="LC2876" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2884
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<pre style="margin: 0;">+<span id="LC2884" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">REVERSE</span></span><span class="p"><span class="idiff">,</span></span><span class="x"><span class="idiff right"> </span></span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
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2885
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<pre style="margin: 0;">+<span id="LC2885" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">NUCLEIC</span></span><span class="o" style="font-weight: 600;">:</span></span>
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2877
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2886
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<pre style="margin: 0;"> <span id="LC2886" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HasPrefix</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2878
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<td class="diff-line-num new_line" data-linenumber="2887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2887
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<pre style="margin: 0;"> <span id="LC2887" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// create one operation per argument, even if under a single -element statement</span></span>
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<td class="diff-line-num old_line" data-linenumber="2879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2879
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<td class="diff-line-num new_line" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2888
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<pre style="margin: 0;"> <span id="LC2888" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">Operation</span><span class="p">{</span><span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;">:</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3349,6 +3358,27 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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3349
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3358
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<pre style="margin: 0;"> <span id="LC3358" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">return</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="x"> </span><span class="no" style="color: teal;">false</span></span>
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3350
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<td class="diff-line-num new_line" data-linenumber="3359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3359
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<pre style="margin: 0;"> <span id="LC3359" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3351
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<td class="diff-line-num new_line" data-linenumber="3360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3360
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<pre style="margin: 0;"> <span id="LC3360" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="3361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3361
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<pre style="margin: 0;">+<span id="LC3361" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// reverseComplement reverse-complements a nucleotide sequence</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3362
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<pre style="margin: 0;">+<span id="LC3362" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="x"> </span><span class="p">{</span></span>
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3363
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<pre style="margin: 0;">+<span id="LC3363" class="line" lang="go"></span>
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3364
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<pre style="margin: 0;">+<span id="LC3364" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">rune</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3365
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<pre style="margin: 0;">+<span id="LC3365" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// reverse sequence letters - middle base in odd-length sequence is not touched, so cannot also complement here</span></span>
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3366
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<pre style="margin: 0;">+<span id="LC3366" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runes</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="x"> </span><span class="o" style="font-weight: 600;"><</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="x"> </span><span class="p">{</span></span>
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3367
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<pre style="margin: 0;">+<span id="LC3367" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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3368
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<pre style="margin: 0;">+<span id="LC3368" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3369
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<pre style="margin: 0;">+<span id="LC3369" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="no" style="color: teal;">false</span></span>
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3370
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<pre style="margin: 0;">+<span id="LC3370" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// now complement every base, also handling uracil, leaving case intact</span></span>
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3371
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<pre style="margin: 0;">+<span id="LC3371" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ch</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="x"> </span><span class="p">{</span></span>
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3372
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<pre style="margin: 0;">+<span id="LC3372" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">revComp</span><span class="p">[</span><span class="n" style="color: #333;">ch</span><span class="p">]</span></span>
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3373
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<pre style="margin: 0;">+<span id="LC3373" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="p">{</span></span>
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3374
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<pre style="margin: 0;">+<span id="LC3374" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="sc" style="color: #d14;">'X'</span></span>
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3375
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<pre style="margin: 0;">+<span id="LC3375" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3376
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<pre style="margin: 0;">+<span id="LC3376" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3377
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<pre style="margin: 0;">+<span id="LC3377" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">(</span><span class="n" style="color: #333;">runes</span><span class="p">)</span></span>
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3378
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<pre style="margin: 0;">+<span id="LC3378" class="line" lang="go"></span>
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3379
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<pre style="margin: 0;">+<span id="LC3379" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">return</span><span class="x"> </span><span class="n" style="color: #333;">str</span></span>
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3380
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<pre style="margin: 0;">+<span id="LC3380" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3381
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<pre style="margin: 0;">+<span id="LC3381" class="line" lang="go"></span>
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3352
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3382
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<pre style="margin: 0;"> <span id="LC3382" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// processElement handles individual -element constructs</span></span>
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3353
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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">processElement</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">))</span><span class="x"> </span><span class="p">{</span></span>
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3384
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<pre style="margin: 0;"> <span id="LC3384" class="line" lang="go"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3467,13 +3497,36 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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3467
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3497
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<pre style="margin: 0;"> <span id="LC3497" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3468
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3498
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<pre style="margin: 0;"> <span id="LC3498" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3469
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3499
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<pre style="margin: 0;"> <span id="LC3499" class="line" lang="go"></span>
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3500
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<pre style="margin: 0;">+<span id="LC3500" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="no" style="color: teal;">false</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3501
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<pre style="margin: 0;">+<span id="LC3501" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="no" style="color: teal;">false</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3502
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<pre style="margin: 0;">+<span id="LC3502" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">status</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="n" style="color: #333;">NUCLEIC</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3503
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<pre style="margin: 0;">+<span id="LC3503" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// -nucleic uses direction of range to decide between forward strand or reverse complement</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3504
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<pre style="margin: 0;">+<span id="LC3504" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span><span class="x"> </span><span class="o" style="font-weight: 600;">></span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="p">{</span></span>
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3505
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<pre style="margin: 0;">+<span id="LC3505" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span></span>
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3506
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<pre style="margin: 0;">+<span id="LC3506" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="no" style="color: teal;">true</span></span>
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3507
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<pre style="margin: 0;">+<span id="LC3507" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3508
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<pre style="margin: 0;">+<span id="LC3508" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="no" style="color: teal;">true</span></span>
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3509
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<pre style="margin: 0;">+<span id="LC3509" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3510
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<pre style="margin: 0;">+<span id="LC3510" class="line" lang="go"></span>
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3470
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<td class="diff-line-num new_line" data-linenumber="3511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3511
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<pre style="margin: 0;"> <span id="LC3511" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// numeric range now calculated, apply slice to string</span></span>
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3471
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<td class="diff-line-num new_line" data-linenumber="3512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3512
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<pre style="margin: 0;"> <span id="LC3512" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3513
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<pre style="margin: 0;">+<span id="LC3513" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3514
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<pre style="margin: 0;">+<span id="LC3514" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3515
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<pre style="margin: 0;">+<span id="LC3515" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3516
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<pre style="margin: 0;">+<span id="LC3516" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="p">{</span></span>
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3517
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<pre style="margin: 0;">+<span id="LC3517" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3518
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<pre style="margin: 0;">+<span id="LC3518" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3472
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<td class="diff-line-num new_line" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3519
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<pre style="margin: 0;"> <span id="LC3519" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3473
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<td class="diff-line-num new_line" data-linenumber="3520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3520
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<pre style="margin: 0;"> <span id="LC3520" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3474
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<td class="diff-line-num new_line" data-linenumber="3521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3521
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<pre style="margin: 0;"> <span id="LC3521" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="x"> </span><span class="o" style="font-weight: 600;">></span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="x"> </span><span class="o" style="font-weight: 600;"><</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3475
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<td class="diff-line-num new_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3522
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<pre style="margin: 0;"> <span id="LC3522" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="3476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3476
</td>
<td class="diff-line-num new_line" data-linenumber="3523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3523
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<pre style="margin: 0;"> <span id="LC3523" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3524
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<pre style="margin: 0;">+<span id="LC3524" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3525
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<pre style="margin: 0;">+<span id="LC3525" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3526
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<pre style="margin: 0;">+<span id="LC3526" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3527
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<pre style="margin: 0;">+<span id="LC3527" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3528
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<pre style="margin: 0;">+<span id="LC3528" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3529
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<pre style="margin: 0;">+<span id="LC3529" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3477
</td>
<td class="diff-line-num new_line" data-linenumber="3530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3530
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3530" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3478
</td>
<td class="diff-line-num new_line" data-linenumber="3531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3531
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<pre style="margin: 0;"> <span id="LC3531" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3479
</td>
<td class="diff-line-num new_line" data-linenumber="3532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3532
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3532" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3481,6 +3534,12 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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<td class="diff-line-num old_line" data-linenumber="3481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3481
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<td class="diff-line-num new_line" data-linenumber="3534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3534
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<pre style="margin: 0;"> <span id="LC3534" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;">></span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;"><=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3482
</td>
<td class="diff-line-num new_line" data-linenumber="3535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3535
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3535" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">max</span><span class="p">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="3483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3483
</td>
<td class="diff-line-num new_line" data-linenumber="3536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3536
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<pre style="margin: 0;"> <span id="LC3536" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3537
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<pre style="margin: 0;">+<span id="LC3537" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3538
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<pre style="margin: 0;">+<span id="LC3538" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3539
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<pre style="margin: 0;">+<span id="LC3539" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3540" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="p">{</span></span>
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3541
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<pre style="margin: 0;">+<span id="LC3541" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3542
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<pre style="margin: 0;">+<span id="LC3542" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3484
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3543
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<pre style="margin: 0;"> <span id="LC3543" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3485
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3544
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<pre style="margin: 0;"> <span id="LC3544" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3486
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3545
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<pre style="margin: 0;"> <span id="LC3545" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3488,6 +3547,12 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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3488
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<td class="diff-line-num new_line" data-linenumber="3547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3547
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<pre style="margin: 0;"> <span id="LC3547" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="x"> </span><span class="o" style="font-weight: 600;"><</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="n" style="color: #333;">min</span><span class="x"> </span><span class="o" style="font-weight: 600;">></span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="n" style="color: #333;">max</span><span class="x"> </span><span class="o" style="font-weight: 600;"><=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3489
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<td class="diff-line-num new_line" data-linenumber="3548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3548
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<pre style="margin: 0;"> <span id="LC3548" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">max</span><span class="p">]</span></span>
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3490
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<td class="diff-line-num new_line" data-linenumber="3549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3549
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<pre style="margin: 0;"> <span id="LC3549" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3550
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<pre style="margin: 0;">+<span id="LC3550" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doRevComp</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3551
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<pre style="margin: 0;">+<span id="LC3551" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3552
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<pre style="margin: 0;">+<span id="LC3552" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3553
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<pre style="margin: 0;">+<span id="LC3553" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doUpCase</span><span class="x"> </span><span class="p">{</span></span>
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3554
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<pre style="margin: 0;">+<span id="LC3554" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3555
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<pre style="margin: 0;">+<span id="LC3555" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3491
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3556
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<pre style="margin: 0;"> <span id="LC3556" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3492
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3557
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<pre style="margin: 0;"> <span id="LC3557" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3493
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3558
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<pre style="margin: 0;"> <span id="LC3558" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3501,8 +3566,8 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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3501
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3566
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<pre style="margin: 0;"> <span id="LC3566" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">sendSlice</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="3502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3502
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<td class="diff-line-num new_line" data-linenumber="3567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3567
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<pre style="margin: 0;"> <span id="LC3567" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="3503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3503
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<td class="diff-line-num new_line" data-linenumber="3568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3568
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<pre style="margin: 0;"> <span id="LC3568" class="line" lang="go"><span class="x"> </span><span class="p">})</span></span>
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3504
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<td class="diff-line-num new_line old" data-linenumber="3569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3504" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3505
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<td class="diff-line-num new_line old" data-linenumber="3569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3505" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">VALUE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3569
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<pre style="margin: 0;">+<span id="LC3569" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">REVERSE</span></span><span class="p"><span class="idiff">,</span></span><span class="x"><span class="idiff right"> </span></span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3570
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<pre style="margin: 0;">+<span id="LC3570" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">VALUE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">NUCLEIC</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="3506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3506
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<td class="diff-line-num new_line" data-linenumber="3571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3571
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<pre style="margin: 0;"> <span id="LC3571" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">exploreElements</span><span class="p">(</span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">lvl</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3507
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<td class="diff-line-num new_line" data-linenumber="3572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3572
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<pre style="margin: 0;"> <span id="LC3572" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3508
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<td class="diff-line-num new_line" data-linenumber="3573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3573
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<pre style="margin: 0;"> <span id="LC3573" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">sendSlice</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3744,7 +3809,7 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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<td class="diff-line-num old_line" data-linenumber="3744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3744
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<td class="diff-line-num new_line" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3809
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<pre style="margin: 0;"> <span id="LC3809" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">single</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3745
</td>
<td class="diff-line-num new_line" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3810
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3810" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">between</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">sep</span></span>
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<td class="diff-line-num old_line" data-linenumber="3746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3746
</td>
<td class="diff-line-num new_line" data-linenumber="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3811
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<pre style="margin: 0;"> <span id="LC3811" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3747
</td>
<td class="diff-line-num new_line old" data-linenumber="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC3747" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">VALUE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3812
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<pre style="margin: 0;">+<span id="LC3812" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">VALUE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">NUCLEIC</span></span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3748
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<td class="diff-line-num new_line" data-linenumber="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3813
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<pre style="margin: 0;"> <span id="LC3813" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">processElement</span><span class="p">(</span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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3749
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<td class="diff-line-num new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3814
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<pre style="margin: 0;"> <span id="LC3814" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3750
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<td class="diff-line-num new_line" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3815
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<pre style="margin: 0;"> <span id="LC3815" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ok</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="no" style="color: teal;">true</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3955,20 +4020,7 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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3955
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<td class="diff-line-num new_line" data-linenumber="4020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4020
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<pre style="margin: 0;"> <span id="LC4020" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="3956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3956
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<td class="diff-line-num new_line" data-linenumber="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4021
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<pre style="margin: 0;"> <span id="LC4021" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ok</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="no" style="color: teal;">true</span></span>
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<td class="diff-line-num old_line" data-linenumber="3957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3957
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<td class="diff-line-num new_line" data-linenumber="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4022
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<pre style="margin: 0;"> <span id="LC4022" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">between</span><span class="p">)</span></span>
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3958
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3958" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">rune</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3959
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3959" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// reverse sequence letters - middle base in odd-length sequence is not touched, so cannot also complement here</span></span>
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3960
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3960" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runes</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="x"> </span><span class="o" style="font-weight: 600;"><</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="x"> </span><span class="p">{</span></span>
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3961
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3961" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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3962
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3962" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3963
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3963" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="no" style="color: teal;">false</span></span>
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3964
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3964" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// now complement every base, also handling uracil, leaving case intact</span></span>
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3965
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3965" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ch</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3966
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3966" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">revComp</span><span class="p">[</span><span class="n" style="color: #333;">ch</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
3967
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3967" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">found</span><span class="x"> </span><span class="p">{</span></span>
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3968
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<td class="diff-line-num new_line old" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3968" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">runes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="sc" style="color: #d14;">'X'</span></span>
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3969
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<pre style="margin: 0;">-<span id="LC3969" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3970
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<pre style="margin: 0;">-<span id="LC3970" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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3971
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<pre style="margin: 0;">-<span id="LC3971" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">(</span><span class="n" style="color: #333;">runes</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4023
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<pre style="margin: 0;">+<span id="LC4023" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3972
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<td class="diff-line-num new_line" data-linenumber="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4024
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<pre style="margin: 0;"> <span id="LC4024" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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3973
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4025
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<pre style="margin: 0;"> <span id="LC4025" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">between</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">sep</span></span>
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3974
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4026
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<pre style="margin: 0;"> <span id="LC4026" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4270,6 +4322,37 @@ func ProcessClause(curr *Node, stages []*Step, mask, prev, pfx, sfx, plg, sep, d</td>
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4270
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4322
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<pre style="margin: 0;"> <span id="LC4322" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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4271
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<td class="diff-line-num new_line" data-linenumber="4323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4323
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<pre style="margin: 0;"> <span id="LC4323" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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4272
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<td class="diff-line-num new_line" data-linenumber="4324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4324
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<pre style="margin: 0;"> <span id="LC4324" class="line" lang="go"><span class="x"> </span><span class="p">})</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4325
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<pre style="margin: 0;">+<span id="LC4325" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">REVERSE</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4326
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<pre style="margin: 0;">+<span id="LC4326" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">processElement</span><span class="p">(</span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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4327
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<pre style="margin: 0;">+<span id="LC4327" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4328
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<pre style="margin: 0;">+<span id="LC4328" class="line" lang="go"></span>
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4329
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<pre style="margin: 0;">+<span id="LC4329" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FieldsFunc</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span><span class="x"> </span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">rune</span><span class="p">)</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4330
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<pre style="margin: 0;">+<span id="LC4330" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">return</span><span class="x"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unicode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IsLetter</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span><span class="x"> </span><span class="o" style="font-weight: 600;">&&</span><span class="x"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">unicode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">IsDigit</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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4331
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<pre style="margin: 0;">+<span id="LC4331" class="line" lang="go"><span class="x"> </span><span class="p">})</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4332
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<pre style="margin: 0;">+<span id="LC4332" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">lf</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">rt</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="x"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">words</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">lf</span><span class="x"> </span><span class="o" style="font-weight: 600;"><</span><span class="x"> </span><span class="n" style="color: #333;">rt</span><span class="p">;</span><span class="x"> </span><span class="n" style="color: #333;">lf</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">rt</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">+</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">rt</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="x"> </span><span class="p">{</span></span>
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4333
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<pre style="margin: 0;">+<span id="LC4333" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="p">[</span><span class="n" style="color: #333;">lf</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="p">[</span><span class="n" style="color: #333;">rt</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="p">[</span><span class="n" style="color: #333;">rt</span><span class="p">],</span><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="p">[</span><span class="n" style="color: #333;">lf</span><span class="p">]</span></span>
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4334
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<pre style="margin: 0;">+<span id="LC4334" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4335
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<pre style="margin: 0;">+<span id="LC4335" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">for</span><span class="x"> </span><span class="n" style="color: #333;">_</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">item</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="k" style="font-weight: 600;">range</span><span class="x"> </span><span class="n" style="color: #333;">words</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4336
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<pre style="margin: 0;">+<span id="LC4336" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">item</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToLower</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4337
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<pre style="margin: 0;">+<span id="LC4337" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">DeStop</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4338
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<pre style="margin: 0;">+<span id="LC4338" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">IsStopWord</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4339
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<pre style="margin: 0;">+<span id="LC4339" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4340
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<pre style="margin: 0;">+<span id="LC4340" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4341
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<pre style="margin: 0;">+<span id="LC4341" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4342
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<pre style="margin: 0;">+<span id="LC4342" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">DoStem</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4343
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<pre style="margin: 0;">+<span id="LC4343" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">item</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">porter2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stem</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4344
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<pre style="margin: 0;">+<span id="LC4344" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">item</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TrimSpace</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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4345
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<pre style="margin: 0;">+<span id="LC4345" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4346
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<pre style="margin: 0;">+<span id="LC4346" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">item</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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4347
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<pre style="margin: 0;">+<span id="LC4347" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">continue</span></span>
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4348
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<pre style="margin: 0;">+<span id="LC4348" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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4349
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<pre style="margin: 0;">+<span id="LC4349" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ok</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="no" style="color: teal;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4350
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<pre style="margin: 0;">+<span id="LC4350" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">between</span><span class="p">)</span></span>
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4351
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<pre style="margin: 0;">+<span id="LC4351" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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4352
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<pre style="margin: 0;">+<span id="LC4352" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">between</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">sep</span></span>
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4353
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<pre style="margin: 0;">+<span id="LC4353" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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4354
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<pre style="margin: 0;">+<span id="LC4354" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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4355
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<pre style="margin: 0;">+<span id="LC4355" class="line" lang="go"><span class="x"> </span><span class="p">})</span></span>
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4273
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4356
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<pre style="margin: 0;"> <span id="LC4356" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="o" style="font-weight: 600;">:</span></span>
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4274
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<td class="diff-line-num new_line" data-linenumber="4357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4357
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<pre style="margin: 0;"> <span id="LC4357" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">processElement</span><span class="p">(</span><span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span><span class="x"> </span><span class="p">{</span></span>
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4275
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4358
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<pre style="margin: 0;"> <span id="LC4358" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">!=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4447,8 +4530,8 @@ func ProcessInstructions(commands []*Operation, curr *Node, mask, tab, ret strin</td>
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4447
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<td class="diff-line-num new_line" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4530
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<pre style="margin: 0;"> <span id="LC4530" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Value</span></span>
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<td class="diff-line-num old_line" data-linenumber="4448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4448
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<td class="diff-line-num new_line" data-linenumber="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4531
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<pre style="margin: 0;"> <span id="LC4531" class="line" lang="go"></span>
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<td class="diff-line-num old_line" data-linenumber="4449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4449
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<td class="diff-line-num new_line" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4532
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<pre style="margin: 0;"> <span id="LC4532" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">switch</span><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Type</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4450
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<td class="diff-line-num new_line old" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4450" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
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4451
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<td class="diff-line-num new_line old" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4451" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="o" style="font-weight: 600;">:</span></span>
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4533
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<pre style="margin: 0;">+<span id="LC4533" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">ELEMENT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">FIRST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LAST</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ENCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UPPER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LOWER</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TITLE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">YEAR</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TRANSLATE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">TERMS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">WORDS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">PAIRS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;"><span class="idiff left">REVERSE</span></span><span class="p"><span class="idiff">,</span></span><span class="x"><span class="idiff right"> </span></span><span class="n" style="color: #333;">LETTERS</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">CLAUSES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INDICES</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MESHCODE</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MATRIX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ACCENTED</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4534
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<pre style="margin: 0;">+<span id="LC4534" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">NUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">LEN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUM</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MAX</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">INC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEC</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">SUB</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">AVG</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">DEV</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">MED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIN</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">BIT</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ZEROBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ONEBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">UCSCBASED</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">REVCOMP</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">NUCLEIC</span></span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="4452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4452
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<td class="diff-line-num new_line" data-linenumber="4535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4535
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4535" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">txt</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">ok</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="n" style="color: #333;">ProcessClause</span><span class="p">(</span><span class="n" style="color: #333;">curr</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stages</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">mask</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">tab</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">pfx</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">sfx</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">plg</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">sep</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">def</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">op</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Type</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">index</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">level</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">variables</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">transform</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4453
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<td class="diff-line-num new_line" data-linenumber="4536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4536
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<pre style="margin: 0;"> <span id="LC4536" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">ok</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4454
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<td class="diff-line-num new_line" data-linenumber="4537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4537
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4537" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">plg</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4474,11 +4557,16 @@ func ProcessInstructions(commands []*Operation, curr *Node, mask, tab, ret strin</td>
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4474
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<td class="diff-line-num new_line" data-linenumber="4557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4557
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<pre style="margin: 0;"> <span id="LC4557" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">LBL</span><span class="o" style="font-weight: 600;">:</span></span>
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4475
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<td class="diff-line-num new_line" data-linenumber="4558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4558
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<pre style="margin: 0;"> <span id="LC4558" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">lbl</span><span class="x"> </span><span class="o" style="font-weight: 600;">:=</span><span class="x"> </span><span class="n" style="color: #333;">str</span></span>
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<td class="diff-line-num old_line" data-linenumber="4476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4476
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<td class="diff-line-num new_line" data-linenumber="4559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4559
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<pre style="margin: 0;"> <span id="LC4559" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">accum</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4560
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<pre style="margin: 0;">+<span id="LC4560" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">accum</span><span class="p">(</span><span class="n" style="color: #333;">plg</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4561
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<pre style="margin: 0;">+<span id="LC4561" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">accum</span><span class="p">(</span><span class="n" style="color: #333;">pfx</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4477
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<td class="diff-line-num new_line" data-linenumber="4562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4562
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<pre style="margin: 0;"> <span id="LC4562" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">plain</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4478
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<td class="diff-line-num new_line" data-linenumber="4563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4563
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<pre style="margin: 0;"> <span id="LC4563" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">accum</span><span class="p">(</span><span class="n" style="color: #333;">lbl</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4479
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<td class="diff-line-num new_line" data-linenumber="4564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4564
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<pre style="margin: 0;"> <span id="LC4564" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4480
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<td class="diff-line-num new_line" data-linenumber="4565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4565
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<pre style="margin: 0;"> <span id="LC4565" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">printInColor</span><span class="p">(</span><span class="n" style="color: #333;">lbl</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="4481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4481
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<td class="diff-line-num new_line" data-linenumber="4566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4566
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<pre style="margin: 0;"> <span id="LC4566" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4567
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<pre style="margin: 0;">+<span id="LC4567" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">accum</span><span class="p">(</span><span class="n" style="color: #333;">sfx</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4568
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<pre style="margin: 0;">+<span id="LC4568" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">plg</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4569
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<pre style="margin: 0;">+<span id="LC4569" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">lst</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">elg</span></span>
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4482
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<td class="diff-line-num new_line" data-linenumber="4570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4570
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<pre style="margin: 0;"> <span id="LC4570" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">tab</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">col</span></span>
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<td class="diff-line-num old_line" data-linenumber="4483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4483
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<td class="diff-line-num new_line" data-linenumber="4571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4571
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<pre style="margin: 0;"> <span id="LC4571" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">ret</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">lin</span></span>
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<td class="diff-line-num old_line" data-linenumber="4484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4484
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4572
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<pre style="margin: 0;"> <span id="LC4572" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">case</span><span class="x"> </span><span class="n" style="color: #333;">PFC</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5697,7 +5785,7 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {</td>
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5697
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5785
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<pre style="margin: 0;"> <span id="LC5785" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-element"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDSeq_accession-version"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-clr"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-rst"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-tab"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">n"</span><span class="p">)</span></span>
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5698
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<td class="diff-line-num new_line" data-linenumber="5786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5786
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<pre style="margin: 0;"> <span id="LC5786" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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5699
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<td class="diff-line-num new_line" data-linenumber="5787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5787
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<pre style="margin: 0;"> <span id="LC5787" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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5700
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<pre style="margin: 0;">-<span id="LC5700" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-pattern"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDSeq"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-ACCN"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDSeq_accession-version"</span><span class="p">)</span></span>
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5788
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<pre style="margin: 0;">+<span id="LC5788" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-pattern"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDSeq"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-ACCN"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDSeq_accession-version"</span><span class="p"><span class="idiff left">,</span></span><span class="x"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">"-SEQ"</span></span><span class="p"><span class="idiff">,</span></span><span class="x"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">"INSDSeq_sequence"</span></span><span class="p">)</span></span>
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5701
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5789
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<pre style="margin: 0;"> <span id="LC5789" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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5702
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5790
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<pre style="margin: 0;"> <span id="LC5790" class="line" lang="go"></span>
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5703
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<td class="diff-line-num new_line" data-linenumber="5791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5791
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<pre style="margin: 0;"> <span id="LC5791" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">doIndex</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5868,6 +5956,30 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {</td>
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5868
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<td class="diff-line-num new_line" data-linenumber="5956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5956
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<pre style="margin: 0;"> <span id="LC5956" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// report capitalization or vocabulary failure</span></span>
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5869
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5957
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<pre style="margin: 0;"> <span id="LC5957" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">checkAgainstVocabulary</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"element"</span><span class="p">,</span><span class="x"> </span><span class="n" style="color: #333;">insdtags</span><span class="p">)</span></span>
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5870
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<td class="diff-line-num new_line" data-linenumber="5958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5958
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<pre style="margin: 0;"> <span id="LC5958" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5959
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<pre style="margin: 0;">+<span id="LC5959" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">str</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="s" style="color: #d14;">"sub_sequence"</span><span class="x"> </span><span class="p">{</span></span>
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5960
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<pre style="margin: 0;">+<span id="LC5960" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="5961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5961
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<pre style="margin: 0;">+<span id="LC5961" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// special sub_sequence qualifier shows sequence under feature intervals</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5962
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<pre style="margin: 0;">+<span id="LC5962" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-block"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDFeature_intervals"</span><span class="p">)</span></span>
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5963
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<pre style="margin: 0;">+<span id="LC5963" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">isPipe</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5964
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<pre style="margin: 0;">+<span id="LC5964" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-lbl"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5965
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<pre style="margin: 0;">+<span id="LC5965" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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5966
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<pre style="margin: 0;">+<span id="LC5966" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-lbl"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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5967
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<pre style="margin: 0;">+<span id="LC5967" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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5968
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<pre style="margin: 0;">+<span id="LC5968" class="line" lang="go"></span>
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5969
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<pre style="margin: 0;">+<span id="LC5969" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-subset"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDInterval"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-FR"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDInterval_from"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-TO"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDInterval_to"</span><span class="p">)</span></span>
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5970
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<pre style="margin: 0;">+<span id="LC5970" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">isPipe</span><span class="x"> </span><span class="p">{</span></span>
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5971
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<pre style="margin: 0;">+<span id="LC5971" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-pfx"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-tab"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-nucleic"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"&SEQ[&FR:&TO]"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5972
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<pre style="margin: 0;">+<span id="LC5972" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5973
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<pre style="margin: 0;">+<span id="LC5973" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-pfx"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-tab"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-nucleic"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">&SEQ[&FR:&TO]</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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5974
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<pre style="margin: 0;">+<span id="LC5974" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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5975
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<pre style="margin: 0;">+<span id="LC5975" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="5976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5976
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<pre style="margin: 0;">+<span id="LC5976" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-subset"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDFeature_intervals"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5977
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5977" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">isPipe</span><span class="x"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5978
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<pre style="margin: 0;">+<span id="LC5978" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-lbl"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t"</span><span class="p">)</span></span>
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5979
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<pre style="margin: 0;">+<span id="LC5979" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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5980
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<pre style="margin: 0;">+<span id="LC5980" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-lbl"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"\\</span><span class="s" style="color: #d14;">t</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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5981
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<pre style="margin: 0;">+<span id="LC5981" class="line" lang="go"><span class="x"> </span><span class="p">}</span></span>
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5982
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<pre style="margin: 0;">+<span id="LC5982" class="line" lang="go"></span>
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5871
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5983
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<pre style="margin: 0;"> <span id="LC5983" class="line" lang="go"><span class="x"> </span><span class="p">}</span><span class="x"> </span><span class="k" style="font-weight: 600;">else</span><span class="x"> </span><span class="p">{</span></span>
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5872
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5984
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<pre style="margin: 0;"> <span id="LC5984" class="line" lang="go"></span>
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5873
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5985
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<pre style="margin: 0;"> <span id="LC5985" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">acc</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="nb" style="color: #0086b3;">append</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"-block"</span><span class="p">,</span><span class="x"> </span><span class="s" style="color: #d14;">"INSDQualifier"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8364,7 +8476,7 @@ func main() {</td>
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8364
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8476
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<pre style="margin: 0;"> <span id="LC8476" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// -e2index shortcut for experimental indexing code (documented in rchive.go)</span></span>
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8365
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8477
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<pre style="margin: 0;"> <span id="LC8477" class="line" lang="go"><span class="x"> </span><span class="k" style="font-weight: 600;">if</span><span class="x"> </span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">0</span><span class="p">]</span><span class="x"> </span><span class="o" style="font-weight: 600;">==</span><span class="x"> </span><span class="s" style="color: #d14;">"-e2index"</span><span class="x"> </span><span class="p">{</span></span>
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8366
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8478
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<pre style="margin: 0;"> <span id="LC8478" class="line" lang="go"></span>
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8367
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<pre style="margin: 0;">-<span id="LC8367" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// e.g., xtract -transform <span class="idiff left right">meshtree.txt</span> -e2index</span></span>
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<pre style="margin: 0;">+<span id="LC8479" class="line" lang="go"><span class="x"> </span><span class="c" style="color: #998; font-style: italic;">// e.g., xtract -transform <span class="idiff left right">"$EDIRECT_MESH_TREE"</span> -e2index</span></span>
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<pre style="margin: 0;"> <span id="LC8480" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC8481" class="line" lang="go"><span class="x"> </span><span class="n" style="color: #333;">args</span><span class="x"> </span><span class="o" style="font-weight: 600;">=</span><span class="x"> </span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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