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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/bfa1bdb45ecf116d953c9f8f19a4a7f7685931e6">bfa1bdb4</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-02-12T12:06:11-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.6.20210209+dfsg</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ef78a8d078d7619d005b8aff1c2d085e1f822d4f">
transmute.go
</a>
</li>
<li class="file-stats">
<a href="#96f5584f0d6dcaca2b56481ad25dbd045758ed30">
xtract.go
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ef78a8d078d7619d005b8aff1c2d085e1f822d4f">
<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/bfa1bdb45ecf116d953c9f8f19a4a7f7685931e6#ef78a8d078d7619d005b8aff1c2d085e1f822d4f"><strong>transmute.go</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,6 +155,8 @@ Sequence Editing</td>
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155
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="go"><span class="s" style="color: #d14;"> -delete Delete N bases</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
156
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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC156" class="line" lang="go"><span class="s" style="color: #d14;"> -insert Insert given sequence</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
157
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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="go"></span>
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<td class="diff-line-num new old_line" data-linenumber="158" style="width: 35px; color: rgba(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="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="go"><span class="s" style="color: #d14;"> -extract Use xtract -insd feat_location instructions</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="go"></span>
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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
158
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="go"><span class="s" style="color: #d14;">Sequence Processing</span></span>
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<td class="diff-line-num old_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">
159
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC161" class="line" lang="go"></span>
</pre>
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<td class="diff-line-num 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">
160
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="go"><span class="s" style="color: #d14;"> -cds2prot Translate coding region into protein</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" style="width: 35px; color: rgba(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="276" style="width: 35px; color: rgba(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">@@ -274,14 +276,14 @@ Mitochondrial Mistranslation</td>
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<td class="diff-line-num new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="go"></span>
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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="go"><span class="s" style="color: #d14;"> efetch -db nuccore -id NC_012920 -format gb |</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="go"><span class="s" style="color: #d14;"> transmute -g2x |</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="go"><span class="s" style="color: #d14;"> xtract -insd CDS gene product translation sub_sequence |</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="go"><span class="s" style="color: #d14;"> while IFS=$'\t' read acc gene prod prot seq</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="go"><span class="s" style="color: #d14;"> xtract -insd CDS gene product <span class="idiff left right">protein_id </span>translation sub_sequence |</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="go"><span class="s" style="color: #d14;"> while IFS=$'\t' read acc gene prod pr<span class="idiff left right">id pr</span>ot seq</span></span>
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279
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="go"><span class="s" style="color: #d14;"> do</span></span>
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280
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<td class="diff-line-num new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="go"><span class="s" style="color: #d14;"> mito=$( echo "$seq" | transmute -cds2prot -code 2 -stop )</span></span>
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<td class="diff-line-num new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="go"><span class="s" style="color: #d14;"> norm=$( echo "$seq" | transmute -cds2prot -code 1 -stop )</span></span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="go"><span class="s" style="color: #d14;"> if [ "$mito" != "$norm" ]</span></span>
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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="go"><span class="s" style="color: #d14;"> then</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="go"><span class="s" style="color: #d14;"> echo ">$acc $gene $prod"</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="go"><span class="s" style="color: #d14;"> echo ">$acc $gene $pr<span class="idiff left right">id $pr</span>od"</span></span>
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285
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="go"><span class="s" style="color: #d14;"> transmute -diff <( echo "$mito" ) <( echo "$norm" )</span></span>
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286
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="go"><span class="s" style="color: #d14;"> echo ""</span></span>
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287
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="go"><span class="s" style="color: #d14;"> fi</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4639" style="width: 35px; color: rgba(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="4641" style="width: 35px; color: rgba(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">@@ -4639,8 +4641,8 @@ func SequenceRemove(inp io.Reader, args []string) {</td>
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4639
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4641
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<pre style="margin: 0;"> <span id="LC4641" class="line" lang="go"> <span class="k" style="font-weight: 600;">return</span></span>
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4640
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4642
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<pre style="margin: 0;"> <span id="LC4642" class="line" lang="go"> <span class="p">}</span></span>
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4641
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4643
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<pre style="margin: 0;"> <span id="LC4643" class="line" lang="go"></span>
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4642
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<pre style="margin: 0;">-<span id="LC4642" class="line" lang="go"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">:=</span> <span class="m" style="color: #099;"><span class="idiff left right">0</span></span></span>
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4643
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<pre style="margin: 0;">-<span id="LC4643" class="line" lang="go"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">:=</span> <span class="m" style="color: #099;"><span class="idiff left right">0</span></span></span>
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4644
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<pre style="margin: 0;">+<span id="LC4644" class="line" lang="go"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span></span>
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4645
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<pre style="margin: 0;">+<span id="LC4645" class="line" lang="go"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span></span>
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4644
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4646
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<pre style="margin: 0;"> <span id="LC4646" class="line" lang="go"></span>
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4647
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<pre style="margin: 0;"> <span id="LC4647" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// skip past command name</span></span>
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4648
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<pre style="margin: 0;"> <span id="LC4648" class="line" lang="go"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4651" style="width: 35px; color: rgba(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">@@ -4649,10 +4651,12 @@ func SequenceRemove(inp io.Reader, args []string) {</td>
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4651
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<pre style="margin: 0;"> <span id="LC4651" class="line" lang="go"></span>
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4650
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4652
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<pre style="margin: 0;"> <span id="LC4652" class="line" lang="go"> <span class="k" style="font-weight: 600;">switch</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="p">{</span></span>
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4651
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4653
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<pre style="margin: 0;"> <span id="LC4653" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-first"</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC4652" class="line" lang="go"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetNumericArg</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bases to delete at beginning"</span><span class="p">,</span> <span class="m" style="color: #099;">0</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="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4654" class="line" lang="go"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetStringArg</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bases to delete at beginning"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4655" class="line" lang="go"> <span class="n" style="color: #333;">first</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;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4656" class="line" lang="go"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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4657
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<pre style="margin: 0;"> <span id="LC4657" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-last"</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC4655" class="line" lang="go"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetNumericArg</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bases to delete at end"</span><span class="p">,</span> <span class="m" style="color: #099;">0</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="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4658
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<pre style="margin: 0;">+<span id="LC4658" class="line" lang="go"> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetStringArg</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">"Bases to delete at end"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4659" class="line" lang="go"> <span class="n" style="color: #333;">last</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;">ToUpper</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span></span>
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4660
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<pre style="margin: 0;"> <span id="LC4660" class="line" lang="go"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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4657
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4661
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<pre style="margin: 0;"> <span id="LC4661" class="line" lang="go"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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4662
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<pre style="margin: 0;"> <span id="LC4662" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Unrecognized option after -remove command</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -4663,21 +4667,63 @@ func SequenceRemove(inp io.Reader, args []string) {</td>
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4667
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<pre style="margin: 0;"> <span id="LC4667" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">ReadAllIntoSequence</span><span class="p">(</span><span class="n" style="color: #333;">inp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4668" class="line" lang="go"></span>
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4669
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<pre style="margin: 0;"> <span id="LC4669" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">:=</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>
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<pre style="margin: 0;">-<span id="LC4666" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC4667" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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4668
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<pre style="margin: 0;">-<span id="LC4668" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC4669" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</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>
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4670
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<pre style="margin: 0;">-<span id="LC4670" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC4671" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -first argument %d is greater than sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC4672" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC4670" class="line" lang="go"></span>
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<pre style="margin: 0;">+<span id="LC4671" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">IsAllDigits</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4672" class="line" lang="go"> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">strconv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Atoi</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">)</span></span>
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4673
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<pre style="margin: 0;">+<span id="LC4673" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">==</span> <span class="no" style="color: #008080;">nil</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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4674
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<pre style="margin: 0;">+<span id="LC4674" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4675
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<pre style="margin: 0;">+<span id="LC4675" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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4676
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<pre style="margin: 0;">+<span id="LC4676" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</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>
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4677
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<pre style="margin: 0;">+<span id="LC4677" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4678
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<pre style="margin: 0;">+<span id="LC4678" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -first argument %d is greater than sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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4679
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<pre style="margin: 0;">+<span id="LC4679" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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4680
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<pre style="margin: 0;">+<span id="LC4680" class="line" lang="go"> <span class="p">}</span></span>
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4681
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<pre style="margin: 0;">+<span id="LC4681" class="line" lang="go"> <span class="p">}</span></span>
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4682
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<pre style="margin: 0;">+<span id="LC4682" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4683
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<pre style="margin: 0;">+<span id="LC4683" class="line" lang="go"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">)</span></span>
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4684
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<pre style="margin: 0;">+<span id="LC4684" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4685
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<pre style="margin: 0;">+<span id="LC4685" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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4686
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<pre style="margin: 0;">+<span id="LC4686" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// warn if existing sequence does not match deletion argument</span></span>
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4687
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<pre style="margin: 0;">+<span id="LC4687" class="line" lang="go"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">:=</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;">val</span><span class="p">]</span></span>
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4688
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<pre style="margin: 0;">+<span id="LC4688" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ext</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4689
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<pre style="margin: 0;">+<span id="LC4689" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">WARNING: -first argument %s does not match existing sequence %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span><span class="p">)</span></span>
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4690
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<pre style="margin: 0;">+<span id="LC4690" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4691
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<pre style="margin: 0;">+<span id="LC4691" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// delete characters</span></span>
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4692
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<pre style="margin: 0;">+<span id="LC4692" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">:</span><span class="p">]</span></span>
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4693
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<pre style="margin: 0;">+<span id="LC4693" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</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>
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4694
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<pre style="margin: 0;">+<span id="LC4694" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4695
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<pre style="margin: 0;">+<span id="LC4695" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -first argument %d is greater than sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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4696
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<pre style="margin: 0;">+<span id="LC4696" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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4697
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<pre style="margin: 0;">+<span id="LC4697" class="line" lang="go"> <span class="p">}</span></span>
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4673
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4698
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<pre style="margin: 0;"> <span id="LC4698" class="line" lang="go"> <span class="p">}</span></span>
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4674
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4699
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<pre style="margin: 0;"> <span id="LC4699" class="line" lang="go"> <span class="p">}</span></span>
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4675
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<pre style="margin: 0;">-<span id="LC4675" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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4676
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<td class="diff-line-num new_line old" data-linenumber="4700" 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="LC4676" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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4677
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<pre style="margin: 0;">-<span id="LC4677" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</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;">ln</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last</span><span class="p">]</span></span>
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4678
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<pre style="margin: 0;">-<span id="LC4678" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4679
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<pre style="margin: 0;">-<span id="LC4679" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -last argument %d is greater than sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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4680
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<pre style="margin: 0;">-<span id="LC4680" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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4700
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<pre style="margin: 0;">+<span id="LC4700" class="line" lang="go"></span>
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4701
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<pre style="margin: 0;">+<span id="LC4701" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">IsAllDigits</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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4702
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<pre style="margin: 0;">+<span id="LC4702" class="line" lang="go"> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">strconv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Atoi</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span></span>
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4703
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<pre style="margin: 0;">+<span id="LC4703" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">==</span> <span class="no" style="color: #008080;">nil</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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4704
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<pre style="margin: 0;">+<span id="LC4704" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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4705
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<pre style="margin: 0;">+<span id="LC4705" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</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;">ln</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">val</span><span class="p">]</span></span>
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4706
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<pre style="margin: 0;">+<span id="LC4706" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4707
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<pre style="margin: 0;">+<span id="LC4707" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -last argument %d is greater than remaining sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4708
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<pre style="margin: 0;">+<span id="LC4708" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4709
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<pre style="margin: 0;">+<span id="LC4709" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4710
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<pre style="margin: 0;">+<span id="LC4710" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4711
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<pre style="margin: 0;">+<span id="LC4711" class="line" lang="go"> <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="4712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4712
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<pre style="margin: 0;">+<span id="LC4712" class="line" lang="go"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4713
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<pre style="margin: 0;">+<span id="LC4713" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4714
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<pre style="margin: 0;">+<span id="LC4714" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4715
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<pre style="margin: 0;">+<span id="LC4715" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// warn if existing sequence does not match deletion argument</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4716
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<pre style="margin: 0;">+<span id="LC4716" class="line" lang="go"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">ln</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">val</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="4717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4717
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<pre style="margin: 0;">+<span id="LC4717" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ext</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4718
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<pre style="margin: 0;">+<span id="LC4718" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">WARNING: -last argument %s does not match existing sequence %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">last</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4719
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<pre style="margin: 0;">+<span id="LC4719" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4720
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<pre style="margin: 0;">+<span id="LC4720" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// delete characters</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4721
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<pre style="margin: 0;">+<span id="LC4721" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</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;">ln</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">val</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4722
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<pre style="margin: 0;">+<span id="LC4722" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</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>
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<td class="diff-line-num new new_line" data-linenumber="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4723
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<pre style="margin: 0;">+<span id="LC4723" class="line" lang="go"> <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="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4724
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<pre style="margin: 0;">+<span id="LC4724" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: -last argument %d is greater than sequence length %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4725
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<pre style="margin: 0;">+<span id="LC4725" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4726
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<pre style="margin: 0;">+<span id="LC4726" class="line" lang="go"> <span class="p">}</span></span>
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4681
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<td class="diff-line-num new_line" data-linenumber="4727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4727
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<pre style="margin: 0;"> <span id="LC4727" class="line" lang="go"> <span class="p">}</span></span>
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4682
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4728
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<pre style="margin: 0;"> <span id="LC4728" class="line" lang="go"> <span class="p">}</span></span>
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4729
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<pre style="margin: 0;"> <span id="LC4729" 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">@@ -4846,6 +4892,77 @@ func SequenceReplace(inp io.Reader, args []string) {</td>
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4846
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4892
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<pre style="margin: 0;"> <span id="LC4892" class="line" lang="go"> <span class="p">}</span></span>
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4847
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4893
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<pre style="margin: 0;"> <span id="LC4893" class="line" lang="go"><span class="p">}</span></span>
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4848
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4894
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<pre style="margin: 0;"> <span id="LC4894" class="line" lang="go"></span>
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4895
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<pre style="margin: 0;">+<span id="LC4895" class="line" lang="go"><span class="k" style="font-weight: 600;">func</span> <span class="n" style="color: #333;">SequenceExtract</span><span class="p">(</span><span class="n" style="color: #333;">inp</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Reader</span><span class="p">,</span> <span class="n" style="color: #333;">args</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span> <span class="p">{</span></span>
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4896
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4897
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<pre style="margin: 0;">+<span id="LC4897" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">inp</span> <span class="o" style="font-weight: 600;">==</span> <span class="no" style="color: #008080;">nil</span> <span class="p">{</span></span>
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4898
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<pre style="margin: 0;">+<span id="LC4898" class="line" lang="go"> <span class="k" style="font-weight: 600;">return</span></span>
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4899
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<pre style="margin: 0;">+<span id="LC4899" class="line" lang="go"> <span class="p">}</span></span>
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4900
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<pre style="margin: 0;">+<span id="LC4900" class="line" lang="go"></span>
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4901
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<pre style="margin: 0;">+<span id="LC4901" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// skip past command name</span></span>
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4902
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<pre style="margin: 0;">+<span id="LC4902" class="line" lang="go"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</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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4903
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<pre style="margin: 0;">+<span id="LC4903" class="line" lang="go"></span>
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4904
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<pre style="margin: 0;">+<span id="LC4904" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</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>
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4905
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<pre style="margin: 0;">+<span id="LC4905" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Missing argument after -extract command</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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4906
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<pre style="margin: 0;">+<span id="LC4906" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Exit</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4907
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<pre style="margin: 0;">+<span id="LC4907" class="line" lang="go"> <span class="p">}</span></span>
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4908
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<pre style="margin: 0;">+<span id="LC4908" class="line" lang="go"></span>
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4909
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<pre style="margin: 0;">+<span id="LC4909" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// read output of xtract -insd feat_location qualifier</span></span>
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4910
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<pre style="margin: 0;">+<span id="LC4910" class="line" lang="go"> <span class="n" style="color: #333;">feat_loc</span> <span class="o" style="font-weight: 600;">:=</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>
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4911
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4912
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<pre style="margin: 0;">+<span id="LC4912" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">ReadAllIntoSequence</span><span class="p">(</span><span class="n" style="color: #333;">inp</span><span class="p">)</span></span>
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4913
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<pre style="margin: 0;">+<span id="LC4913" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4914
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<pre style="margin: 0;">+<span id="LC4914" class="line" lang="go"> <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">:=</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>
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4915
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<pre style="margin: 0;">+<span id="LC4915" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4916
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<pre style="margin: 0;">+<span id="LC4916" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// split intervals, e.g., "201..224,1550..1920,1986..2085,2317..2404,2466..2629"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4917
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<pre style="margin: 0;">+<span id="LC4917" class="line" lang="go"> <span class="n" style="color: #333;">comma</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;">Split</span><span class="p">(</span><span class="n" style="color: #333;">feat_loc</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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4918
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<pre style="margin: 0;">+<span id="LC4918" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4919
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<pre style="margin: 0;">+<span id="LC4919" class="line" lang="go"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">item</span> <span class="o" style="font-weight: 600;">:=</span> <span class="k" style="font-weight: 600;">range</span> <span class="n" style="color: #333;">comma</span> <span class="p">{</span></span>
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4920
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<pre style="margin: 0;">+<span id="LC4920" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4921
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<pre style="margin: 0;">+<span id="LC4921" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// also allow dash separator, e.g., "201-224,1550-1920,1986-2085,2317-2404,2466-2629"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4922
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<pre style="margin: 0;">+<span id="LC4922" class="line" lang="go"> <span class="n" style="color: #333;">item</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;">Replace</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">".."</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>
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4923
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<pre style="margin: 0;">+<span id="LC4923" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4924
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<pre style="margin: 0;">+<span id="LC4924" class="line" lang="go"> <span class="n" style="color: #333;">fr</span><span class="p">,</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">SplitInTwoAt</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">,</span> <span class="s" style="color: #d14;">".."</span><span class="p">,</span> <span class="n" style="color: #333;">LEFT</span><span class="p">)</span></span>
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4925
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<pre style="margin: 0;">+<span id="LC4925" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4926
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<pre style="margin: 0;">+<span id="LC4926" class="line" lang="go"> <span class="n" style="color: #333;">fr</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;">TrimSpace</span><span class="p">(</span><span class="n" style="color: #333;">fr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4927
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<pre style="margin: 0;">+<span id="LC4927" class="line" lang="go"> <span class="n" style="color: #333;">to</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;">TrimSpace</span><span class="p">(</span><span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4928
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<pre style="margin: 0;">+<span id="LC4928" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4929
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<pre style="margin: 0;">+<span id="LC4929" class="line" lang="go"> <span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">strconv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Atoi</span><span class="p">(</span><span class="n" style="color: #333;">fr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4930
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<pre style="margin: 0;">+<span id="LC4930" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">!=</span> <span class="no" style="color: #008080;">nil</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4931
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<pre style="margin: 0;">+<span id="LC4931" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Unrecognized number '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4932
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<pre style="margin: 0;">+<span id="LC4932" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Exit</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4933
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<pre style="margin: 0;">+<span id="LC4933" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4934
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<pre style="margin: 0;">+<span id="LC4934" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4935
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<pre style="margin: 0;">+<span id="LC4935" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Starting point '%s' out of range</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">fr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4936
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<pre style="margin: 0;">+<span id="LC4936" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Exit</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4937
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<pre style="margin: 0;">+<span id="LC4937" class="line" lang="go"> <span class="p">}</span></span>
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4938
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<pre style="margin: 0;">+<span id="LC4938" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="4939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4939
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<pre style="margin: 0;">+<span id="LC4939" class="line" lang="go"> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">strconv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Atoi</span><span class="p">(</span><span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4940
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<pre style="margin: 0;">+<span id="LC4940" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">!=</span> <span class="no" style="color: #008080;">nil</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4941
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<pre style="margin: 0;">+<span id="LC4941" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Unrecognized number '%s'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4942
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<pre style="margin: 0;">+<span id="LC4942" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Exit</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4943
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<pre style="margin: 0;">+<span id="LC4943" class="line" lang="go"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4944
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<pre style="margin: 0;">+<span id="LC4944" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ln</span> <span class="p">{</span></span>
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4945
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<pre style="margin: 0;">+<span id="LC4945" class="line" lang="go"> <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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ERROR: Ending point '%s' out of range</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">)</span></span>
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4946
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<pre style="margin: 0;">+<span id="LC4946" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Exit</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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4947
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<pre style="margin: 0;">+<span id="LC4947" class="line" lang="go"> <span class="p">}</span></span>
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4948
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<pre style="margin: 0;">+<span id="LC4948" class="line" lang="go"></span>
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4949
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<pre style="margin: 0;">+<span id="LC4949" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</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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4950
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<pre style="margin: 0;">+<span id="LC4950" class="line" lang="go"> <span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">--</span></span>
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4951
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<pre style="margin: 0;">+<span id="LC4951" class="line" lang="go"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">:=</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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4952
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<pre style="margin: 0;">+<span id="LC4952" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stdout</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;">sub</span><span class="p">)</span></span>
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4953
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<pre style="margin: 0;">+<span id="LC4953" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</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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4954
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<pre style="margin: 0;">+<span id="LC4954" class="line" lang="go"> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">--</span></span>
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4955
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<pre style="margin: 0;">+<span id="LC4955" class="line" lang="go"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">str</span><span class="p">[</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">min</span><span class="p">]</span></span>
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4956
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<pre style="margin: 0;">+<span id="LC4956" class="line" lang="go"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">)</span></span>
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4957
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<pre style="margin: 0;">+<span id="LC4957" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stdout</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;">sub</span><span class="p">)</span></span>
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4958
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<pre style="margin: 0;">+<span id="LC4958" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4959
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<pre style="margin: 0;">+<span id="LC4959" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// need more information to know strand if single point</span></span>
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4960
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<pre style="margin: 0;">+<span id="LC4960" class="line" lang="go"> <span class="p">}</span></span>
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4961
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<pre style="margin: 0;">+<span id="LC4961" class="line" lang="go"> <span class="p">}</span></span>
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4962
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<pre style="margin: 0;">+<span id="LC4962" class="line" lang="go"></span>
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4963
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<pre style="margin: 0;">+<span id="LC4963" class="line" lang="go"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Stdout</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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4964
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<pre style="margin: 0;">+<span id="LC4964" class="line" lang="go"><span class="p">}</span></span>
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4965
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<pre style="margin: 0;">+<span id="LC4965" class="line" lang="go"></span>
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4849
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4966
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<pre style="margin: 0;"> <span id="LC4966" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// REVERSE SEQUENCE</span></span>
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4850
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4967
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<pre style="margin: 0;"> <span id="LC4967" class="line" lang="go"></span>
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4851
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4968
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<pre style="margin: 0;"> <span id="LC4968" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// SeqFlip reverses without complementing - e.g., minus strand proteins translated in reverse order</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">@@ -4958,7 +5075,7 @@ func PrintFastaPairs(frst, scnd string) {</td>
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4958
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5075
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<pre style="margin: 0;"> <span id="LC5075" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// print in blocks of 50 bases or residues</span></span>
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4959
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5076
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<pre style="margin: 0;"> <span id="LC5076" class="line" lang="go"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">:=</span> <span class="m" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mx</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="m" style="color: #099;">50</span> <span class="p">{</span></span>
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4960
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5077
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<pre style="margin: 0;"> <span id="LC5077" class="line" lang="go"> <span class="n" style="color: #333;">dl</span> <span class="o" style="font-weight: 600;">:=</span> <span class="m" style="color: #099;">50</span></span>
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4961
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<pre style="margin: 0;">-<span id="LC4961" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mx</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="m" style="color: #099;">50</span> <span class="p">{</span></span>
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5078
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<pre style="margin: 0;">+<span id="LC5078" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mx</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="m" style="color: #099;">50</span> <span class="p">{</span></span>
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4962
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5079
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<pre style="margin: 0;"> <span id="LC5079" class="line" lang="go"> <span class="n" style="color: #333;">dl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mx</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span></span>
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4963
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5080
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<pre style="margin: 0;"> <span id="LC5080" class="line" lang="go"> <span class="p">}</span></span>
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4964
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5081
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<pre style="margin: 0;"> <span id="LC5081" class="line" lang="go"> <span class="n" style="color: #333;">lf</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">fs</span><span class="p">[</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">dl</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">@@ -8344,6 +8461,8 @@ func main() {</td>
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8344
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8461
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<pre style="margin: 0;"> <span id="LC8461" class="line" lang="go"> <span class="n" style="color: #333;">SequenceRetain</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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8345
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<td class="diff-line-num new_line" data-linenumber="8462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8462
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<pre style="margin: 0;"> <span id="LC8462" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-replace"</span><span class="o" style="font-weight: 600;">:</span></span>
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8346
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8463
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<pre style="margin: 0;"> <span id="LC8463" class="line" lang="go"> <span class="n" style="color: #333;">SequenceReplace</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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8464
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<pre style="margin: 0;">+<span id="LC8464" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-extract"</span><span class="o" style="font-weight: 600;">:</span></span>
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8465
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<pre style="margin: 0;">+<span id="LC8465" class="line" lang="go"> <span class="n" style="color: #333;">SequenceExtract</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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8347
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8466
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<pre style="margin: 0;"> <span id="LC8466" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-revcomp"</span><span class="o" style="font-weight: 600;">:</span></span>
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8348
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8467
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<pre style="margin: 0;"> <span id="LC8467" class="line" lang="go"> <span class="n" style="color: #333;">NucRevComp</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">)</span></span>
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8349
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8468
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<pre style="margin: 0;"> <span id="LC8468" class="line" lang="go"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"-reverse"</span><span class="o" style="font-weight: 600;">:</span></span>
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<a href="https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/bfa1bdb45ecf116d953c9f8f19a4a7f7685931e6#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">@@ -276,7 +276,7 @@ Command Generator</td>
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276
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="go"><span class="s" style="color: #d14;"> Descriptors INSDSeq_sequence INSDSeq_definition INSDSeq_division</span></span>
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277
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="go"><span class="s" style="color: #d14;"> Flags [complete|partial]</span></span>
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278
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="go"><span class="s" style="color: #d14;"> Feature(s) CDS,mRNA</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="go"><span class="s" style="color: #d14;"> Qualifiers INSDFeature_key "#INSDInterval" gene product sub_sequence</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="go"><span class="s" style="color: #d14;"> Qualifiers INSDFeature_key "#INSDInterval" gene product <span class="idiff left right">feat_location </span>sub_sequence</span></span>
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280
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="go"></span>
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281
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="go"><span class="s" style="color: #d14;">Variation Processing</span></span>
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="go"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6340" style="width: 35px; color: rgba(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">@@ -6340,6 +6340,66 @@ func ProcessINSD(args []string, isPipe, addDash, doIndex bool) []string {</td>
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6340
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6340
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<pre style="margin: 0;"> <span id="LC6340" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-deq"</span><span class="p">,</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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6341
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6341
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<pre style="margin: 0;"> <span id="LC6341" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6343" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"feat_location"</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC6345" class="line" lang="go"> <span class="c" style="color: #998; font-style: italic;">// special feat_location qualifier shows feature intervals</span></span>
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<pre style="margin: 0;">+<span id="LC6346" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-block"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDFeature_intervals"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6348" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-subset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDInterval"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-FR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDInterval_from"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-TO"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDInterval_to"</span><span class="p">)</span></span>
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6349
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<pre style="margin: 0;">+<span id="LC6349" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isPipe</span> <span class="p">{</span></span>
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6350
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<pre style="margin: 0;">+<span id="LC6350" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-pfx"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"-tab"</span><span class="p">,</span> <span class="s" style="color: #d14;">".."</span><span class="p">,</span> <span class="s" style="color: #d14;">"-element"</span><span class="p">,</span> <span class="s" style="color: #d14;">"&FR"</span><span class="p">)</span></span>
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6351
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<pre style="margin: 0;">+<span id="LC6351" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-pfx"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"-tab"</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="s" style="color: #d14;">"-element"</span><span class="p">,</span> <span class="s" style="color: #d14;">"&TO"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6352" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6353
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<pre style="margin: 0;">+<span id="LC6353" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-pfx"</span><span class="p">,</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="s" style="color: #d14;">"-tab"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</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="s" style="color: #d14;">"-element"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">&FR</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6354" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-pfx"</span><span class="p">,</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="s" style="color: #d14;">"-tab"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</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="s" style="color: #d14;">"-element"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">&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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<pre style="margin: 0;">+<span id="LC6355" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6357" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-subset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDFeature_intervals"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6358" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isPipe</span> <span class="p">{</span></span>
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6359
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<pre style="margin: 0;">+<span id="LC6359" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-deq"</span><span class="p">,</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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<pre style="margin: 0;">+<span id="LC6360" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6361
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<pre style="margin: 0;">+<span id="LC6361" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-deq"</span><span class="p">,</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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6362
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<pre style="margin: 0;">+<span id="LC6362" class="line" lang="go"> <span class="p">}</span></span>
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6363
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<pre style="margin: 0;">+<span id="LC6363" class="line" lang="go"></span>
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6364
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<pre style="margin: 0;">+<span id="LC6364" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="6365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6365
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<pre style="margin: 0;">+<span id="LC6365" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"chloroplast"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6366
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<pre style="margin: 0;">+<span id="LC6366" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"chromoplast"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6367
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<pre style="margin: 0;">+<span id="LC6367" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"cyanelle"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6368
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<pre style="margin: 0;">+<span id="LC6368" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"environmental_sample"</span> <span class="o" style="font-weight: 600;">||</span></span>
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6369
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<pre style="margin: 0;">+<span id="LC6369" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"focus"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6370
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<pre style="margin: 0;">+<span id="LC6370" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"germline"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6371
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<pre style="margin: 0;">+<span id="LC6371" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"kinetoplast"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6372
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<pre style="margin: 0;">+<span id="LC6372" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"macronuclear"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6373
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<pre style="margin: 0;">+<span id="LC6373" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"metagenomic"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6374
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<pre style="margin: 0;">+<span id="LC6374" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"mitochondrion"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6375
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<pre style="margin: 0;">+<span id="LC6375" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"partial"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6376
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<pre style="margin: 0;">+<span id="LC6376" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"proviral"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6377
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<pre style="margin: 0;">+<span id="LC6377" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pseudo"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6378
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<pre style="margin: 0;">+<span id="LC6378" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rearranged"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6379
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<pre style="margin: 0;">+<span id="LC6379" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ribosomal_slippage"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6380
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<pre style="margin: 0;">+<span id="LC6380" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"trans_splicing"</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6381
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<pre style="margin: 0;">+<span id="LC6381" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transgenic"</span> <span class="o" style="font-weight: 600;">||</span></span>
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6382
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<pre style="margin: 0;">+<span id="LC6382" class="line" lang="go"> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"virion"</span> <span class="p">{</span></span>
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6383
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<pre style="margin: 0;">+<span id="LC6383" class="line" lang="go"></span>
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<td class="diff-line-num new new_line" data-linenumber="6384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6384
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<pre style="margin: 0;">+<span id="LC6384" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-block"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier"</span><span class="p">)</span></span>
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6385
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<pre style="margin: 0;">+<span id="LC6385" class="line" lang="go"></span>
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6386
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<pre style="margin: 0;">+<span id="LC6386" class="line" lang="go"> <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="s" style="color: #d14;">"qualifier"</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="p">)</span></span>
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6387
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<pre style="margin: 0;">+<span id="LC6387" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">doIndex</span> <span class="p">{</span></span>
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6388
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<pre style="margin: 0;">+<span id="LC6388" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-if"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-equals"</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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6389
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<pre style="margin: 0;">+<span id="LC6389" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-clr"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-indices"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier_name"</span><span class="p">)</span></span>
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6390
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<pre style="margin: 0;">+<span id="LC6390" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6391
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<pre style="margin: 0;">+<span id="LC6391" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-if"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-equals"</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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6392
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<pre style="margin: 0;">+<span id="LC6392" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-lbl"</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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6393
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<pre style="margin: 0;">+<span id="LC6393" class="line" lang="go"> <span class="p">}</span></span>
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6394
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<pre style="margin: 0;">+<span id="LC6394" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">addDash</span> <span class="p">{</span></span>
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6395
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<pre style="margin: 0;">+<span id="LC6395" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-block"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDFeature"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-unless"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-equals"</span><span class="p">,</span> <span class="n" style="color: #333;">str</span><span class="p">)</span></span>
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6396
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<pre style="margin: 0;">+<span id="LC6396" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isPipe</span> <span class="p">{</span></span>
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6397
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<pre style="margin: 0;">+<span id="LC6397" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-lbl"</span><span class="p">,</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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6398
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<pre style="margin: 0;">+<span id="LC6398" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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6399
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<pre style="margin: 0;">+<span id="LC6399" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-lbl"</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"\\</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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6400
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<pre style="margin: 0;">+<span id="LC6400" class="line" lang="go"> <span class="p">}</span></span>
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6401
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<pre style="margin: 0;">+<span id="LC6401" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6402" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC6403" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6404" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC6405" class="line" lang="go"> <span class="n" style="color: #333;">acc</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">"-block"</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSDQualifier"</span><span class="p">)</span></span>
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