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<h3>
Aaron M. Ucko pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/1309b538c6bfc80bc3052d7fd88cdb2ffe890a0d">1309b538</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-10-25T18:27:58-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.11.3+dfsg</pre>
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<h4>6 changed files:</h4>
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<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#c9512c0b1798e84b5d6a945ad880784dab140a53">
build/Makefile.vers
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<a href="#4705a68e02a22c6bfea0273af010dd42e1861b4a">
shared/toolkit.vers
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<li class="file-stats">
<a href="#5cd76f234790117309267153be422c6d4e826541">
shared/toolkit.vers.h
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<a href="#14865266faebea48f0221b2afc675b1d701f864b">
tools/driver-tool/imp_fasterq_dump.cpp
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/1309b538c6bfc80bc3052d7fd88cdb2ffe890a0d#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># NCBI External Developer Release:</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.11.3</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**October 25, 2021**</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**fasterq-dump, sratools**</span>: fasta and fasta-unsorted parameters work correctly </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.11.2</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**October 7, 2021**</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/1309b538c6bfc80bc3052d7fd88cdb2ffe890a0d#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -15,14 +15,12 @@ using data in the INSDC Sequence Read Archives.</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### ANNOUNCEMENT:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">October 7, 2021</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our <span class="p">[</span><span class="nv" style="color: #008080;">data format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/</span><span class="p">)</span> page.</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">October 25, 2021. SRA Toolkit 2.11.3:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">fixed a bug in fasterq-dump: fasta and fasta-unsorted parameters work correctly.</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">October 7, 2021. SRA Toolkit 2.11.2:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">October 7, 2021: SRA Toolkit 2.11.2.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">SRA data are now available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete more rapidly. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users that do not require full base quality scores for their analysis can request the SRA Lite version to save time on their data transfers. To request the SRA Lite data when using the SRA toolkit, set the "Prefer SRA Lite files with simplified base quality scores" option on the main page of the toolkit configuration- this will instruct the tools to preferentially use the SRA Lite format when available (please be sure to use toolkit version 2.11.2 or later to access this feature). The quality scores generated from SRA Lite files will be the same for each base within a given read (quality = 30 or 3, depending on whether the Read Filter flag is set to 'pass' or 'reject'). Data in the SRA Normalized Format with full base quality scores will continue to have a .sra file extension, while the SRA Lite files have a .sralite file extension. For more information please see our <span class="p">[</span><span class="nv" style="color: #008080;">data format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.ncbi.nlm.nih.gov/sra/docs/sra-data-formats/</span><span class="p">)</span> page.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">August 17, 2021: SRA Toolkit 2.11.1.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/1309b538c6bfc80bc3052d7fd88cdb2ffe890a0d#c9512c0b1798e84b5d6a945ad880784dab140a53"><strong>build/Makefile.vers</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,4 +23,4 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ===========================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># SRA-TOOLS and library version</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.11.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.11.<span class="idiff left right">3</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.11.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.11.<span class="idiff left right">3</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020B000<span class="idiff left right">2</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020B000<span class="idiff left right">3</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/1309b538c6bfc80bc3052d7fd88cdb2ffe890a0d#14865266faebea48f0221b2afc675b1d701f864b"><strong>tools/driver-tool/imp_fasterq_dump.cpp</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">@@ -168,6 +168,8 @@ struct FasterqParams final : CmnOptAndAccessions</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">strict</span> <span class="p">)</span> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"strict"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bases</span><span class="p">.</span><span class="n" style="color: #333;">isEmpty</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"bases : "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">append</span> <span class="p">)</span> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"append"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">fasta</span> <span class="p">)</span> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"fasta"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">fastaUnsorted</span> <span class="p">)</span> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"fasta-unsorted"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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171
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CmnOptAndAccessions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">show</span><span class="p">(</span><span class="n" style="color: #333;">ss</span><span class="p">);</span></span>
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172
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="p">}</span></span>
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173
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -208,6 +210,8 @@ struct FasterqParams final : CmnOptAndAccessions</td>
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208
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">strict</span> <span class="p">)</span> <span class="n" style="color: #333;">builder</span> <span class="p">.</span> <span class="n" style="color: #333;">add_option</span><span class="p">(</span> <span class="s" style="color: #d14;">"--strict"</span> <span class="p">);</span></span>
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209
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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bases</span><span class="p">.</span><span class="n" style="color: #333;">isEmpty</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">builder</span> <span class="p">.</span> <span class="n" style="color: #333;">add_option</span><span class="p">(</span> <span class="s" style="color: #d14;">"-B"</span><span class="p">,</span> <span class="n" style="color: #333;">bases</span> <span class="p">);</span></span>
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210
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">append</span> <span class="p">)</span> <span class="n" style="color: #333;">builder</span> <span class="p">.</span> <span class="n" style="color: #333;">add_option</span><span class="p">(</span> <span class="s" style="color: #d14;">"-A"</span> <span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">fasta</span> <span class="p">)</span> <span class="n" style="color: #333;">builder</span> <span class="p">.</span> <span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--fasta"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">fastaUnsorted</span> <span class="p">)</span> <span class="n" style="color: #333;">builder</span> <span class="p">.</span> <span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--fasta-unsorted"</span><span class="p">);</span></span>
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211
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="p">}</span></span>
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212
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>
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213
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">check</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">override</span></span>
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