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GitLab

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<h3>

Steffen Möller pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/salmon">Debian Med / salmon</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf">fdb785fc</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2021-12-13T15:40:52+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.0+ds1</pre>

</li>

</ul>

<h4>27 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#34ffb03041dc818ba71da0518ec52a0134f543f8">

current_version.txt

</a>

</li>

<li class="file-stats">

<a href="#5a1b92f4d2201f84f3ab9bfe7917ee0a5531e53d">

doc/source/alevin.rst

</a>

</li>

<li class="file-stats">

<a href="#9d4e8ab62832d7b298261aae1fe1123d28783525">

doc/source/conf.py

</a>

</li>

<li class="file-stats">

<a href="#8ffde13df31f212345642ccfa4755f3bd99e7e61">

docker/Dockerfile

</a>

</li>

<li class="file-stats">

<a href="#3cbc10c17d78796adbdc9a8a8b8702f83a02d41f">

docker/build_test.sh

</a>

</li>

<li class="file-stats">

<a href="#1fe0f4d55f3b84573f46c3b205cdf1546c6f1595">

include/AlevinUtils.hpp

</a>

</li>

<li class="file-stats">

<a href="#584b1766692e6054a45025e3ab2a1cc01e4508f1">

include/ReadExperiment.hpp

</a>

</li>

<li class="file-stats">

<a href="#b28e1098f756957ff90d12768200c4e9602817b4">

include/SalmonConfig.hpp

</a>

</li>

<li class="file-stats">

<a href="#44e448f604f7e82906787f365f589a3ea4657ba9">

include/SalmonDefaults.hpp

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<li class="file-stats">

<a href="#775cca6353faebf70ff10a2f9d1684153c93c4ac">

include/SalmonIndex.hpp

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<li class="file-stats">

<a href="#8ed491100d2189e665edcdee1d3d3c1bf51ac354">

include/SingleCellProtocols.hpp

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<li class="file-stats">

<a href="#ed5b323fc76589e9d58c007363dc77aab1e0fe6d">

include/cuckoohash_map.hh

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<li class="file-stats">

<a href="#7f5cd5d35adbd8144fe2dbe27ee0f99655bfab85">

include/json.hpp

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<li class="file-stats">

<a href="#d9225c32d4f01af48593b4d164c0276ef713fb37">

scripts/fetchPufferfish.sh

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<li class="file-stats">

<a href="#8fdbe631bc12d59b3cea9274359041cf09b11240">

src/Alevin.cpp

</a>

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<li class="file-stats">

<a href="#9fcb6347f66e2015a27d89eec62944e82352b5d9">

src/AlevinHash.cpp

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<li class="file-stats">

<a href="#d95dc025bfe71cabe95139b51ea263244f8cbab2">

src/AlevinUtils.cpp

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<li class="file-stats">

<a href="#2d5e0752f505025e2570ff24aee737c61f0ebcdd">

src/BuildSalmonIndex.cpp

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<li class="file-stats">

<a href="#4d255e86e1e69399b0a00c7213bf7ae26df399d4">

src/CollapsedCellOptimizer.cpp

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<li class="file-stats">

<a href="#3bcd26cb8cf945e15663285c1e7eeb25ccc7e9be">

src/GZipWriter.cpp

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<li class="file-stats">

<a href="#f172e578ce4bd88dde4a1e5db8b0748de9bb9a18">

src/ProgramOptionsGenerator.cpp

</a>

</li>

<li class="file-stats">

<a href="#56c25523d0e5423ba1e491804ea1df82bdaf152b">

src/Salmon.cpp

</a>

</li>

<li class="file-stats">

<a href="#f6eb2d02fae3bac60ea268026fe2765f446b2a4d">

src/SalmonAlevin.cpp

</a>

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<li class="file-stats">

<a href="#048f27201dad07181046acde7ff740937d795521">

src/SalmonQuantMerge.cpp

</a>

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<li class="file-stats">

<a href="#50bd7b80772108780ea31715fa1e48fc1610d64e">

src/SalmonQuantify.cpp

</a>

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<li class="file-stats">

<a href="#271fbfae8ef9baaaaa6c951017faa5e410641190">

src/SalmonQuantifyAlignments.cpp

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<li class="file-stats">

<a href="#4da84e41d07b7f0b42dd57e484cdc5f4c6f8a496">

src/WhiteList.cpp

</a>

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</ul>

<h4>Changes:</h4>

<li id="34ffb03041dc818ba71da0518ec52a0134f543f8">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#34ffb03041dc818ba71da0518ec52a0134f543f8"><strong>current_version.txt</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">VERSION_MAJOR 1</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">VERSION_MINOR <span class="idiff left right">5</span></span>

</pre>

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3

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">VERSION_PATCH <span class="idiff left right">2</span></span></pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">VERSION_MINOR <span class="idiff left right">6</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">VERSION_PATCH <span class="idiff left right">0</span></span></pre>

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</table>

<br>

</li>

<li id="5a1b92f4d2201f84f3ab9bfe7917ee0a5531e53d">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#5a1b92f4d2201f84f3ab9bfe7917ee0a5531e53d"><strong>doc/source/alevin.rst</strong></a>

<hr>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Alevin</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">================</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

</pre>

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4

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<td class="new_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Alevin is a tool --- integrated with the salmon software --- that introduces a family of algorithms for quantification and analysis of 3' tagged-end single-cell sequencing data. Currently alevin supports the following <span class="idiff left right">two major droplet based </span>single-cell protocols:</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Alevin is a tool --- integrated with the salmon software --- that introduces a family of algorithms for quantification and analysis of 3' tagged-end single-cell sequencing data. Currently alevin supports the following single-cell protocols:</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">1. Drop-seq</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2. 10x-Chromium v1/2/3</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">3. inDropV2</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">4. CELSeq 1/2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">5. Quartz-Seq2</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">6. sci-RNA-seq3</span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Alevin works under the same indexing scheme (as salmon) for the reference, and consumes the set of FASTA/Q files(s) containing the Cellular Barcode(CB) + Unique Molecule identifier (UMI) in one read file and the read sequence in the other.  Given just the transcriptome and the raw read files, alevin generates a cell-by-gene count matrix (in a fraction of the time compared to other tools).</span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></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">@@ -177,6 +181,18 @@ map end-to-end.  Instead, the score of the mapping will be the position along th</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">highest score.  This is the score which must reach the fraction threshold for the read to be considered</span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">as valid.</span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">Single-cell protocol specific notes</span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">------------------------------------</span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">In cases where single-cell protocol supports variable length cellbarcodes, alevin adds nucleotide padding to make the lengths uniform.</span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">Furthermore, the padding scheme ensures that there are no collisions added in the process. The padding scheme is as follows:</span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">1. sci-RNA-seq3: The barcode is composed of 9-10 bp hairpin adaptor and 10 bp reverse transcription index making it 19-20 bp long. If </span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">the bacode is 20 bp long, alevin adds `A` and it adds `AC` if it is 19 bp long. Thus, the length of barcode in the output is 21 bp. </span>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">2. inDropV2: 8-11 bp barcode1 along with 8 bp barcode2 makes up the barcode. For barcode lengths of 16, 17, 18, and 19 bp, alevin adds</span>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">`AAAC`, `AAG`, `AT`, and `A` respectively. Thus, the length of barcode in the output is 20 bp. Furthermore, the position of barcode1 is</span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">dependent on finding exact match of sequence `w1`. If exact match is not found, a search for `w1` is performed allowing a maximum hamming</span>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> distance 2 b/w `w1` and read2 substring of w1 length within the required bounds; the first match is returned.  </span>

</pre>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="plaintext">Output</span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext">------</span>

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<br>

</li>

<li id="9d4e8ab62832d7b298261aae1fe1123d28783525">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#9d4e8ab62832d7b298261aae1fe1123d28783525"><strong>doc/source/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(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">@@ -48,16 +48,16 @@ master_doc = 'index'</td>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'Salmon'</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="51" 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="LC51" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2013-201<span class="idiff left right">7</span>, Rob Patro, Geet Duggal, Mike Love, Rafael Irizarry and Carl Kingsford'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2013-20<span class="idiff left right">2</span>1, Rob Patro, Geet Duggal, Mike Love, Rafael Irizarry and Carl Kingsford'</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># built documents.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">5</span>'</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">6</span>'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="60" 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="LC60" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">5.2</span>'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.<span class="idiff left right">6.0</span>'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>

</pre>

</td>

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<br>

</li>

<li id="8ffde13df31f212345642ccfa4755f3bd99e7e61">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#8ffde13df31f212345642ccfa4755f3bd99e7e61"><strong>docker/Dockerfile</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" style="width: 35px; color: rgba(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="6" style="width: 35px; color: rgba(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">@@ -6,7 +6,7 @@ MAINTAINER salmon.maintainer@gmail.com</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="docker"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker">    ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget</span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> SALMON_VERSION 1.<span class="idiff left right">5.2</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> SALMON_VERSION 1.<span class="idiff left right">6.0</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="docker"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># salmon binary will be installed in /home/salmon/bin/salmon</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="docker"></span>

</pre>

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<br>

</li>

<li id="3cbc10c17d78796adbdc9a8a8b8702f83a02d41f">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#3cbc10c17d78796adbdc9a8a8b8702f83a02d41f"><strong>docker/build_test.sh</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(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="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash</span></span>

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<td class="new_line diff-line-num old" data-linenumber="2" 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="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">SALMON_VERSION</span><span class="o" style="font-weight: 600;">=</span>1.<span class="idiff left right">5.2</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(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="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">SALMON_VERSION</span><span class="o" style="font-weight: 600;">=</span>1.<span class="idiff left right">6.0</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(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="LC3" class="line" lang="shell">docker build <span class="nt" style="color: #000080;">--no-cache</span> <span class="nt" style="color: #000080;">-t</span> combinelab/salmon:<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SALMON_VERSION</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-t</span> combinelab/salmon:latest <span class="nb" style="color: #0086b3;">.</span></span></pre>

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<br>

</li>

<li id="1fe0f4d55f3b84573f46c3b205cdf1546c6f1595">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#1fe0f4d55f3b84573f46c3b205cdf1546c6f1595"><strong>include/AlevinUtils.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <numeric></span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "spdlog/spdlog.h"</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(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="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +73,8 @@ namespace alevin{</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">readWhitelist</span><span class="p">(</span><span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filePath</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp">                       <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hammingDistance</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s2</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">ProtocolT</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(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="LC80" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(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="100" style="width: 35px; color: rgba(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">@@ -97,7 +100,7 @@ namespace alevin{</td>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp">                      <span class="n" style="color: #333;">OrderedOptionsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">os</span><span class="p">(</span><span class="n" style="color: #333;">cmdInfoPath</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">      <span class="n" style="color: #333;">cereal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">JSONOutputArchive</span> <span class="n" style="color: #333;">oa</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp">      <span class="n" style="color: #333;">oa</span><span class="p">(</span><span class="n" style="color: #333;">cereal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_nvp</span><span class="p">(</span><span class="s" style="color: #d14;">"salmon_version<span class="idiff left right">:</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">salmon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version</span><span class="p">)));</span></span>

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(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="LC103" class="line" lang="cpp">      <span class="n" style="color: #333;">oa</span><span class="p">(</span><span class="n" style="color: #333;">cereal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_nvp</span><span class="p">(</span><span class="s" style="color: #d14;">"salmon_version"</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">salmon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version</span><span class="p">)));</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">.</span><span class="n" style="color: #333;">options</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp">          <span class="n" style="color: #333;">oa</span><span class="p">(</span><span class="n" style="color: #333;">cereal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_nvp</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">string_key</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">()));</span></span>

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<br>

</li>

<li id="584b1766692e6054a45025e3ab2a1cc01e4508f1">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#584b1766692e6054a45025e3ab2a1cc01e4508f1"><strong>include/ReadExperiment.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,6 +25,7 @@</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Boost includes</span></span>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem/path.hpp></span></span>

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/range/irange.hpp></span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Cereal includes</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(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="49" style="width: 35px; color: rgba(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">@@ -48,10 +49,12 @@ class ReadExperiment {</td>

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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="cpp"><span class="nl">public:</span></span>

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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">  <span class="n" style="color: #333;">ReadExperiment</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ReadLibrary</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">readLibraries</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// const boost::filesystem::path& transcriptFile,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp">                 <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">                 <span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">                 <span class="c1" style="color: #998; font-style: italic;">// const boost::filesystem::path& indexDirectory,</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">                 <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readLibraries_</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// transcriptFile_(transcriptFile),</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">        <span class="n" style="color: #333;">salmonIndex_</span><span class="p">(</span><span class="n" style="color: #333;">salmonIndex</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">        <span class="n" style="color: #333;">transcripts_</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Transcript</span><span class="o" style="font-weight: 600;">></span><span class="p">()),</span> <span class="n" style="color: #333;">totalAssignedFragments_</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">        <span class="n" style="color: #333;">fragStartDists_</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="n" style="color: #333;">posBiasFW_</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="n" style="color: #333;">posBiasRC_</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="n" style="color: #333;">posBiasExpectFW_</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">        <span class="n" style="color: #333;">posBiasExpectRC_</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="cm" style="color: #998; font-style: italic;">/*seqBiasModel_(1.0),*/</span> <span class="n" style="color: #333;">eqBuilder_</span><span class="p">(</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">maxHashResizeThreads</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">@@ -115,24 +118,6 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    }</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    */</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// ==== Figure out the index type</span></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">versionPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"versionInfo.json"</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp">    <span class="n" style="color: #333;">SalmonIndexVersionInfo</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp">    <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">versionPath</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexVersion</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">      <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MemoryWriter</span> <span class="n" style="color: #333;">infostr</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp">      <span class="n" style="color: #333;">infostr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: The index version file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">versionPath</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" doesn't seem to exist.  Please try re-building the salmon "</span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp">                 <span class="s" style="color: #d14;">"index."</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="127" 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="LC127" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span><span class="n" style="color: #333;">infostr</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="LC128" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check index version compatibility here</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">indexType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// ==== Figure out the index type</span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp">    <span class="n" style="color: #333;">salmonIndex_</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SalmonIndex</span><span class="p">(</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="p">,</span> <span class="n" style="color: #333;">indexType</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp">    <span class="n" style="color: #333;">salmonIndex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">indexDirectory</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Now we'll have either an FMD-based index or a QUASI index</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(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="LC122" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// dispatch on the correct type.</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="cpp">    <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MemoryWriter</span> <span class="n" style="color: #333;">infostr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,7 +144,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Create the cluster forest for this set of transcripts</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="n" style="color: #333;">clusters_</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ClusterForest</span><span class="p">(</span><span class="n" style="color: #333;">transcripts_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">transcripts_</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp">  <span class="n" style="color: #333;">EQBuilderT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">equivalenceClassBuilder</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">eqBuilder_</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getIndexSeqHash256</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonIndex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqHash256</span><span class="p">();</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp">  <span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">getIndex</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff right">()</span>;</span> <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">  <span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">getIndex</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">PuffIndexT</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">loadTranscriptsFromPuff</span><span class="p">(</span><span class="n" style="color: #333;">PuffIndexT</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx_</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">atomic</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">burnedIn</span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp">        <span class="n" style="color: #333;">totalAssignedFragments_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numAssignedFragments_</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">numBurninFrags</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rl</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readLibraries_</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="404" 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="LC419" class="line" lang="cpp">      <span class="n" style="color: #333;">processReadLibrary</span><span class="p">(</span><span class="n" style="color: #333;">rl</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">transcripts_</span><span class="p">,</span> <span class="n" style="color: #333;">clusterForest</span><span class="p">(),</span></span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp">      <span class="n" style="color: #333;">processReadLibrary</span><span class="p">(</span><span class="n" style="color: #333;">rl</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p">,</span> <span class="n" style="color: #333;">transcripts_</span><span class="p">,</span> <span class="n" style="color: #333;">clusterForest</span><span class="p">(),</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(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="LC405" class="line" lang="cpp">                         <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">fragLengthDist_</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">()),</span> <span class="n" style="color: #333;">numAssignedFragments_</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp">                         <span class="n" style="color: #333;">numThreads</span><span class="p">,</span> <span class="n" style="color: #333;">burnedIn</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="806" style="width: 35px; color: rgba(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="791" style="width: 35px; color: rgba(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">@@ -806,7 +791,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   * The index we've built on the set of transcripts.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC793" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   */</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="794" 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="LC809" class="line" lang="cpp">  <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p">{</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(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="LC794" class="line" lang="cpp">  <span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="n" style="color: #333;">salmonIndex_</span><span class="p">{</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">};</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(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="LC795" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(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="LC796" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   * The cluster forest maintains the dynamic relationship</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(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="LC797" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">   * defined by transcripts and reads --- if two transcripts</span></span>

</pre>

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<br>

</li>

<li id="b28e1098f756957ff90d12768200c4e9602817b4">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#b28e1098f756957ff90d12768200c4e9602817b4"><strong>include/SalmonConfig.hpp</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">salmon</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">majorVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">minorVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">5</span>"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">patchVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">2</span>"</span><span class="p">;</span></span>

</pre>

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31

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">version</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">5.2</span>"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">minorVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">6</span>"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">patchVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">version</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">6.0</span>"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">indexVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">constexpr</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">requiredQuasiIndexVersion</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"p7"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace salmon</span></span>

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<br>

</li>

<li id="44e448f604f7e82906787f365f589a3ea4657ba9">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#44e448f604f7e82906787f365f589a3ea4657ba9"><strong>include/SalmonDefaults.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(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="140" style="width: 35px; color: rgba(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">@@ -140,6 +140,7 @@ namespace defaults {</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCELSeq</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCELSeq2</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isQuartzSeq2</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(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="LC143" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSciSeq3</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noQuant</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">dumpFQ</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">constexpr</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">dumpArborescences</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

</pre>

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<br>

</li>

<li id="775cca6353faebf70ff10a2f9d1684153c93c4ac">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#775cca6353faebf70ff10a2f9d1684153c93c4ac"><strong>include/SalmonIndex.hpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="246" style="width: 35px; color: rgba(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="246" style="width: 35px; color: rgba(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">@@ -246,4 +246,9 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">decoyNameHash256_</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(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="LC247" class="line" lang="cpp"><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(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="LC248" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Convenience function to load an index</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(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="LC250" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"><span class="n" style="color: #333;">checkLoadIndex</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">               <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">spdlog</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">logger</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif //__SALMON_INDEX_HPP</span></span></pre>

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<li id="8ed491100d2189e665edcdee1d3d3c1bf51ac354">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#8ed491100d2189e665edcdee1d3d3c1bf51ac354"><strong>include/SingleCellProtocols.hpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" style="width: 35px; color: rgba(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="124" style="width: 35px; color: rgba(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">@@ -124,17 +124,19 @@ namespace alevin{</td>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">      <span class="n" style="color: #333;">DropSeq</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">(</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">BarcodeEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span><span class="p">,</span> <span class="mi" style="color: #099;">16777216</span><span class="p">){}</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="127" 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="LC127" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">InDrop</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="128" 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="LC128" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//InDrop starts from 5end with variable</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//length barcodes so provide the full</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// length of the barcod eincluding w1.</span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// UMI length is 6</span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp">      <span class="n" style="color: #333;">InDrop</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">(</span><span class="mi" style="color: #099;">42</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">BarcodeEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span><span class="p">,</span> <span class="mi" style="color: #099;">22347776</span><span class="p">){}</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">InDropV2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//InDropV2 starts from 5end with variable</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//length barcodes where barcode1 varies from 8 to 11 bp</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// followed by w1 sequence, 8 bp barcode2 and 6bp UMI</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">      <span class="n" style="color: #333;">InDropV2</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="n" style="color: #333;">BarcodeEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span><span class="p">,</span> <span class="mi" style="color: #099;">22347776</span><span class="p">){}</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">w1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">w1Length</span><span class="p">,</span> <span class="n" style="color: #333;">maxHammingDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">bc2Len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setW1</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">w1_</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp">        <span class="n" style="color: #333;">w1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w1_</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">        <span class="n" style="color: #333;">w1Length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w1</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">w1Pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bc2EndPos</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(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="LC142" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CITESeq</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(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">@@ -179,7 +181,14 @@ namespace alevin{</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Custom</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(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="LC182" class="line" lang="cpp">      <span class="n" style="color: #333;">Custom</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">BarcodeEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">){}</span></span>

</pre>

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181

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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

183

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp">    <span class="p">};</span></span>

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<td class="new_line diff-line-num old" data-linenumber="184" 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="LC182" class="line" lang="cpp">    </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(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="LC184" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SciSeq3</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">      <span class="n" style="color: #333;">SciSeq3</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Rule</span><span class="p">(</span><span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">BarcodeEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span><span class="p">,</span> <span class="mi" style="color: #099;">1073741824</span><span class="p">){}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(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="LC186" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">anchorSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CAGAGC"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(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="LC187" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">anchorSeqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">anchorSeq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">      <span class="n" style="color: #333;">u_int16_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">maxHairpinIndexLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">      <span class="n" style="color: #333;">u_int16_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">rtIdxLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// rev transcription index length</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

193

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// for the new type of specification</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CustomGeometry</span> <span class="p">{</span></span>

</pre>

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</li>

<li id="ed5b323fc76589e9d58c007363dc77aab1e0fe6d">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#ed5b323fc76589e9d58c007363dc77aab1e0fe6d"><strong>include/cuckoohash_map.hh</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">@@ -113,7 +113,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp">        <span class="n" style="color: #333;">maximum_hashpower_</span><span class="p">(</span><span class="n" style="color: #333;">NO_MAXIMUM_HASHPOWER</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp">        <span class="n" style="color: #333;">max_num_worker_threads_</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(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="LC115" class="line" lang="cpp">    <span class="n" style="color: #333;">all_locks_</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">bucket_count</span><span class="p">(),</span> <span class="n" style="color: #333;">size_type</span><span class="p">(</span><span class="n" style="color: #333;">kMaxNumLocks</span><span class="p">)),</span></span>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp">                            <span class="n" style="color: #333;"><span class="idiff left">spinlock</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

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<td class="old_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(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="LC116" class="line" lang="cpp">                            <span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp">  <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -695,7 +695,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">add_locks_from_other</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cuckoohash_map</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp">    <span class="n" style="color: #333;">locks_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">other_locks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">get_current_locks</span><span class="p">();</span></span>

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<td class="old_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="698" 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="LC698" class="line" lang="cpp">    <span class="n" style="color: #333;">all_locks_</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">other_locks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;"><span class="idiff left">spinlock</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp">    <span class="n" style="color: #333;">all_locks_</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">other_locks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

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<td class="new_line diff-line-num" data-linenumber="699" style="width: 35px; color: rgba(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="LC699" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">other_locks</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">other_locks</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC700" class="line" lang="cpp">              <span class="n" style="color: #333;">get_current_locks</span><span class="p">().</span><span class="n" style="color: #333;">begin</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="cpp">  <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">@@ -794,7 +794,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC794" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// under this lock. One can compute the size of the table by summing the</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(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="LC795" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// elem_counter over all locks.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(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="LC796" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="797" 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="LC797" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// - is_migrated: When resizing with cuckoo_fast_dou<span class="idiff left right">l</span>be, we do not</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(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="LC797" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// - is_migrated: When resizing with cuckoo_fast_doub<span class="idiff left right">l</span>e, we do not</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(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="LC798" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// immediately rehash elements from the old buckets array to the new one.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(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="LC799" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Instead, we'll mark all of the locks as not migrated. So anybody trying to</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(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="LC800" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// acquire the lock must also migrate the corresponding buckets if</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC1823" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1825" class="line" lang="cpp">    <span class="n" style="color: #333;">locks_t</span> <span class="n" style="color: #333;">new_locks</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">size_type</span><span class="p">(</span><span class="n" style="color: #333;">kMaxNumLocks</span><span class="p">),</span> <span class="n" style="color: #333;">new_bucket_count</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1826" 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="LC1826" class="line" lang="cpp">                      <span class="n" style="color: #333;"><span class="idiff left">spinlock</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1827" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1826" class="line" lang="cpp">                      <span class="n" style="color: #333;">get_allocator</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">new_locks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">current_locks</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">current_locks</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">current_locks</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">new_locks</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">spinlock</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">lock</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">new_locks</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="7f5cd5d35adbd8144fe2dbe27ee0f99655bfab85">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#7f5cd5d35adbd8144fe2dbe27ee0f99655bfab85"><strong>include/json.hpp</strong></a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="d9225c32d4f01af48593b4d164c0276ef713fb37">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#d9225c32d4f01af48593b4d164c0276ef713fb37"><strong>scripts/fetchPufferfish.sh</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,11 +22,11 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-fr</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INSTALL_DIR</span><span class="k" style="font-weight: 600;">}</span>/src/pufferfish</span>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">SVER</span><span class="o" style="font-weight: 600;">=</span>salmon-v1.<span class="idiff left right">5.2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">SVER</span><span class="o" style="font-weight: 600;">=</span>salmon-v1.<span class="idiff left right">6.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#SVER=develop</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#SVER=sketch-mode</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">EXPECTED_SHA256</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">86c7ff465d40b8184dca7f6afee693ad1db63be5bf63242161ea39d3507d6d25</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">EXPECTED_SHA256</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(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="LC30" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(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="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXTERNAL_DIR</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(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="LC32" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-k</span> <span class="nt" style="color: #000080;">-L</span> https://github.com/COMBINE-lab/pufferfish/archive/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SVER</span><span class="k" style="font-weight: 600;">}</span>.zip <span class="nt" style="color: #000080;">-o</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">EXTERNAL_DIR</span><span class="k" style="font-weight: 600;">}</span>/pufferfish.zip</span>

</pre>

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<br>

</li>

<li id="8fdbe631bc12d59b3cea9274359041cf09b11240">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#8fdbe631bc12d59b3cea9274359041cf09b11240"><strong>src/Alevin.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,7 @@</td>

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"><HEADER</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">**/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <atomic></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// salmon includes</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "FastxParser.hpp"</span></span>

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ProgramOptionsGenerator.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonConfig.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonDefaults.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonOpts.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonUtils.hpp"</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ProgramOptionsGenerator.hpp"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">paired_parser_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_parser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastxParser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fastx_parser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadQualPair</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">single_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastx_parser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastxParser</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fastx_parser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReadSeq</span><span class="o" style="font-weight: 600;">></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(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">@@ -78,20 +79,18 @@ namespace apt = alevin::protocols;</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">aut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">utils</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">ProtocolT</span><span class="p">></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp">                    <span class="n" style="color: #333;"><span class="idiff left">SalmonOpts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sopt</span></span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp">                    <span class="n" style="color: #333;"><span class="idiff left">boo</span>st</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff">program_options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">parsed_options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orderedOptions</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(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="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">SalmonOpts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sopt</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(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="LC83" class="line" lang="cpp">                    <span class="n" style="color: #333;"><span class="idiff left">boost</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">program_options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">parsed_options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orderedOptions</span></span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(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="LC84" class="line" lang="cpp">                    <span class="n" style="color: #333;">st<span class="idiff left">d</span></span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">ProtocolT</span><span class="p">></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="86" 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="LC86" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="88" 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="LC88" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="89" 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="LC89" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(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="LC87" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(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="LC88" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(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="LC89" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(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="LC90" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">numLowConfidentBarco</span>de</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(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="LC92" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numLowConfidentBarcode</span></span><span class="p"><span class="idiff right">,</span></span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">                <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">salmonIn</span>de<span class="idiff right">x</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//colors for progress monitoring</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">RESET_COLOR</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\x1b</span><span class="s" style="color: #d14;">[0m"</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="835" style="width: 35px; color: rgba(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="834" style="width: 35px; color: rgba(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">@@ -835,7 +834,8 @@ void initiatePipeline(AlevinOpts<ProtocolT>& aopt,</td>

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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp">                      <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp">                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp">                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC838" class="line" lang="cpp">                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readFiles</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp">                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readFiles</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(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="LC838" class="line" lang="cpp">                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC839" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isOptionsOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC840" 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;">isOptionsOk</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp">    <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="894" style="width: 35px; color: rgba(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="894" style="width: 35px; color: rgba(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">@@ -894,14 +894,14 @@ void initiatePipeline(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// write out the cmd_info.json to make sure we have that</span></span>

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<td class="old_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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<pre style="margin: 0;"> <span id="LC895" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">outputDirectory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"output"</span><span class="p">].</span><span class="n" style="color: #333;">as</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;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

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<td class="new_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(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="LC896" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isWriteOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeCmdInfo</span><span class="p">(</span><span class="n" style="color: #333;">outputDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"cmd_info.json"</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

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<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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<pre style="margin: 0;"> <span id="LC898" 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;">isWriteOk</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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<td class="new_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp">      <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Writing cmd_info.json in output directory failed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Exiting now."</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

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<td class="new_line diff-line-num" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp">      <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

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<td class="new_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

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<td class="new_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

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<td class="new_line diff-line-num" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

903

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<pre style="margin: 0;"> <span id="LC903" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// do the actual mapping</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="903" 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">

903

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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC903" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="904" 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">

904

</td>

<td class="new_line diff-line-num old" data-linenumber="904" 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="LC904" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

904

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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

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<td class="new_line diff-line-num" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

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<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="new_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

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<pre style="margin: 0;"> <span id="LC906" class="line" lang="cpp">      <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"sc-align successful."</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="949" style="width: 35px; color: rgba(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="949" style="width: 35px; color: rgba(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">@@ -949,7 +949,7 @@ void initiatePipeline(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(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="LC949" class="line" lang="cpp">    <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Done with Barcode Processing; Moving to Quantify</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(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="LC950" class="line" lang="cpp">    <span class="n" style="color: #333;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">barcodeSoftMap</span><span class="p">,</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="951" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="951" style="width: 35px; color: rgba(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="LC951" class="line" lang="cpp">                <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="952" 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">

952

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<td class="new_line diff-line-num old" data-linenumber="952" 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="LC952" class="line" lang="cpp">                <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="953" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(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="LC952" class="line" lang="cpp">                <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

953

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<td class="new_line diff-line-num" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

953

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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

954

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<td class="new_line diff-line-num" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

954

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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

955

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<td class="new_line diff-line-num" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

955

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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">cmdInfoPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"output"</span><span class="p">].</span><span class="n" style="color: #333;">as</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;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="962" style="width: 35px; color: rgba(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="962" style="width: 35px; color: rgba(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">@@ -962,7 +962,7 @@ void initiatePipeline(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

962

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<td class="new_line diff-line-num" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

962

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<pre style="margin: 0;"> <span id="LC962" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="963" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="963" style="width: 35px; color: rgba(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="LC963" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="964" style="width: 35px; color: rgba(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="LC964" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="965" 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="LC965" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonBarcoding</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(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="LC965" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonBarcoding</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

966

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<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">bfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="p">;</span></span>

</pre>

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967

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<td class="new_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

967

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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

968

</td>

<td class="new_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

968

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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1022" style="width: 35px; color: rgba(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="1022" style="width: 35px; color: rgba(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">@@ -1022,7 +1022,7 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<td class="old_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1023

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<td class="new_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1023

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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

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<td class="new_line diff-line-num" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">dropseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"dropseq"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1025" 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">

1025

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<td class="new_line diff-line-num old" data-linenumber="1025" 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="LC1025" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">indrop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"indrop"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1025

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">indrop<span class="idiff left">V2</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"indrop<span class="idiff right">V2</span>"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

</td>

<td class="new_line diff-line-num" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">citeseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"citeseq"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

</td>

<td class="new_line diff-line-num" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1027

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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chromV3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"chromiumV3"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

</td>

<td class="new_line diff-line-num" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1028

</td>

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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"chromium"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1030" style="width: 35px; color: rgba(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="1030" style="width: 35px; color: rgba(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">@@ -1030,6 +1030,7 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<td class="old_line diff-line-num" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

</td>

<td class="new_line diff-line-num" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1030

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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">celseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"celseq"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

</td>

<td class="new_line diff-line-num" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1031

</td>

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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">celseq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"celseq2"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

</td>

<td class="new_line diff-line-num" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1032" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">quartzseq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"quartzseq2"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1033

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sciseq3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"sciseq3"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

<td class="new_line diff-line-num" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">custom_old</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"barcodeLength"</span><span class="p">)</span> <span class="n" style="color: #333;">and</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

<td class="new_line diff-line-num" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1035

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1035" class="line" lang="cpp">                   <span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"umiLength"</span><span class="p">)</span> <span class="n" style="color: #333;">and</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1035

</td>

<td class="new_line diff-line-num" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1036

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1036" class="line" lang="cpp">                   <span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"end"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1039" style="width: 35px; color: rgba(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="1040" style="width: 35px; color: rgba(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">@@ -1039,7 +1040,7 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1039

</td>

<td class="new_line diff-line-num" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1040

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1040

</td>

<td class="new_line diff-line-num" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1041

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1041

</td>

<td class="new_line diff-line-num" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1042

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dropseq</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1042" 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">

1042

</td>

<td class="new_line diff-line-num old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1042" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">indrop</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1043

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">indrop<span class="idiff left right">V2</span></span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1043

</td>

<td class="new_line diff-line-num" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1044

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1044" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">citeseq</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">noTgMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1044

</td>

<td class="new_line diff-line-num" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1045" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chromV3</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="new_line diff-line-num" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1047" style="width: 35px; color: rgba(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="1048" style="width: 35px; color: rgba(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">@@ -1047,6 +1048,7 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1047

</td>

<td class="new_line diff-line-num" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">celseq</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

</td>

<td class="new_line diff-line-num" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1049

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">celseq2</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1049

</td>

<td class="new_line diff-line-num" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1050" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">quartzseq2</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1051

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sciseq3</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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1050

</td>

<td class="new_line diff-line-num" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">custom</span><span class="p">)</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

</td>

<td class="new_line diff-line-num" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1053

</td>

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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

</td>

<td class="new_line diff-line-num" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">validate_num_protocols</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1077" style="width: 35px; color: rgba(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="1079" style="width: 35px; color: rgba(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">@@ -1077,22 +1079,20 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<td class="old_line diff-line-num" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

</td>

<td class="new_line diff-line-num" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1079

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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using DropSeq Setting for Alevin");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1078

</td>

<td class="new_line diff-line-num" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1080

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1080" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1079

</td>

<td class="new_line diff-line-num" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1081

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1081" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1080" 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">

1080

</td>

<td class="new_line diff-line-num old" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1080" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1082

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1081

</td>

<td class="new_line diff-line-num" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1083

</td>

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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1082" 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">

1082

</td>

<td class="new_line diff-line-num old" data-linenumber="1084" 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="LC1082" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indrop</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1083" 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">

1083

</td>

<td class="new_line diff-line-num old" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1083" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">"Indrop get neighbors removed, please use other protocols"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1084" 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">

1084

</td>

<td class="new_line diff-line-num old" data-linenumber="1084" 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="LC1084" class="line" lang="cpp">      <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1084

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">indropV2</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1085

</td>

<td class="new_line diff-line-num" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1085

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1085" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"w1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1086

</td>

<td class="new_line diff-line-num" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1086

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1086" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">w1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"w1"</span><span class="p">].</span><span class="n" style="color: #333;">as</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;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1087" 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">

1087

</td>

<td class="new_line diff-line-num old" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1087" class="line" lang="cpp">        <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1087

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp">        <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1088

</td>

<td class="new_line diff-line-num" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1088

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1088" class="line" lang="cpp">        <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">setW1</span><span class="p">(</span><span class="n" style="color: #333;">w1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1089" 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">

1089

</td>

<td class="new_line diff-line-num old" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1089" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using InDrop Setting for Alevin");</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1089

</td>

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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using InDrop<span class="idiff left right">V2</span> Setting for Alevin");</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1090

</td>

<td class="new_line diff-line-num" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1090

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1090" class="line" lang="cpp">        <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1091

</td>

<td class="new_line diff-line-num" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1091

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1091" class="line" lang="cpp">                         <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1092" 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">

1092

</td>

<td class="new_line diff-line-num old" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1092" class="line" lang="cpp">                         <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1092

</td>

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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp">                         <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1093

</td>

<td class="new_line diff-line-num" data-linenumber="1093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1093

</td>

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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1094

</td>

<td class="new_line diff-line-num" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1094

</td>

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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1095" 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">

1095

</td>

<td class="new_line diff-line-num old" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1095" class="line" lang="cpp">        <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"ERROR: indrop needs w1 flag too.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Exiting Now"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1095

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp">        <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"ERROR: indrop<span class="idiff left right">V2</span> needs w1 flag too.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Exiting Now"</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1096

</td>

<td class="new_line diff-line-num" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1096

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1096" class="line" lang="cpp">        <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

</td>

<td class="new_line diff-line-num" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1097" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

<td class="new_line diff-line-num" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1102" style="width: 35px; color: rgba(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="1102" style="width: 35px; color: rgba(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">@@ -1102,10 +1102,10 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<td class="old_line diff-line-num" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1102

</td>

<td class="new_line diff-line-num" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1102

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp">        <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">setFeatureLength</span><span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"featureLength"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1103

</td>

<td class="new_line diff-line-num" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1103

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp">        <span class="n" style="color: #333;">aopt</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">setFeatureStart</span><span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">[</span><span class="s" style="color: #d14;">"featureStart"</span><span class="p">].</span><span class="n" style="color: #333;">as</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1104

</td>

<td class="new_line diff-line-num" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1104

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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1105" 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">

1105

</td>

<td class="new_line diff-line-num old" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using InDrop Setting for Alevin");</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1105

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using InDrop<span class="idiff left right">V2</span> Setting for Alevin");</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1106

</td>

<td class="new_line diff-line-num" data-linenumber="1106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1106

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1106" class="line" lang="cpp">        <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1107

</td>

<td class="new_line diff-line-num" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1107

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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="cpp">                         <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1108" 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">

1108

</td>

<td class="new_line diff-line-num old" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1108" class="line" lang="cpp">                         <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1108

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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp">                         <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

</td>

<td class="new_line diff-line-num" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1110

</td>

<td class="new_line diff-line-num" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1110

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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1111

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<td class="new_line diff-line-num" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1111

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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp">        <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"ERROR: citeseq needs featureStart and featureLength flag too.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Exiting Now"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1117" style="width: 35px; color: rgba(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="1117" style="width: 35px; color: rgba(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">@@ -1117,54 +1117,60 @@ salmon-based processing of single-cell RNA-seq data.</td>

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<td class="old_line diff-line-num" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1117

</td>

<td class="new_line diff-line-num" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1117

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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using 10x v3 Setting for Alevin");</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

</td>

<td class="new_line diff-line-num" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

</td>

<td class="new_line diff-line-num" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1120" 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">

1120

</td>

<td class="new_line diff-line-num old" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1120" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1120

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1121

</td>

<td class="new_line diff-line-num" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1121

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1122

</td>

<td class="new_line diff-line-num" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1122

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1122" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1123

</td>

<td class="new_line diff-line-num" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1123

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1123" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1124

</td>

<td class="new_line diff-line-num" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1124

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using 10x v2 Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1125

</td>

<td class="new_line diff-line-num" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1125

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1125" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

</td>

<td class="new_line diff-line-num" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1126" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1127" 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">

1127

</td>

<td class="new_line diff-line-num old" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1127" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1127

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1128

</td>

<td class="new_line diff-line-num" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1128

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1128" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1129

</td>

<td class="new_line diff-line-num" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1129

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1129" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gemcode</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1130

</td>

<td class="new_line diff-line-num" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1130

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1130" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gemcode</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1131

</td>

<td class="new_line diff-line-num" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1131

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using 10x v1 Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1132

</td>

<td class="new_line diff-line-num" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1132

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1133

</td>

<td class="new_line diff-line-num" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1133

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1134" 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">

1134

</td>

<td class="new_line diff-line-num old" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1134" class="line" lang="cpp">                       <span class="n" style="color: #333;">unmateFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1134

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp">                       <span class="n" style="color: #333;">unmateFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1135

</td>

<td class="new_line diff-line-num" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1135

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1136

</td>

<td class="new_line diff-line-num" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1136

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1136" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">celseq</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

</td>

<td class="new_line diff-line-num" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1138

</td>

<td class="new_line diff-line-num" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1138

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using CEL-Seq Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1139

</td>

<td class="new_line diff-line-num" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1139

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1140

</td>

<td class="new_line diff-line-num" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1140

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1140" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1141" 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">

1141

</td>

<td class="new_line diff-line-num old" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1141" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1141

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

</td>

<td class="new_line diff-line-num" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1142

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

</td>

<td class="new_line diff-line-num" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1143

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">celseq2</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1144

</td>

<td class="new_line diff-line-num" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1144

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq2</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1145

</td>

<td class="new_line diff-line-num" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1145

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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using CEL-Seq2 Setting for Alevin");</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1146

</td>

<td class="new_line diff-line-num" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1146

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1147

</td>

<td class="new_line diff-line-num" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1147

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1148" 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">

1148

</td>

<td class="new_line diff-line-num old" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1148" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1148

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1149

</td>

<td class="new_line diff-line-num" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1149

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1149" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1150

</td>

<td class="new_line diff-line-num" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1150

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">quartzseq2</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1151

</td>

<td class="new_line diff-line-num" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1151

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

</td>

<td class="new_line diff-line-num" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1152

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using Quartz-Seq2 Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1153

</td>

<td class="new_line diff-line-num" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1153

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1153" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1154

</td>

<td class="new_line diff-line-num" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1154

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1154" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1155

</td>

<td class="new_line diff-line-num old" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1155" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1155

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1156

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1156" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">sciseq3</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1157

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1158

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1158" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using Sci-Seq3 Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1159

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1160

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1161

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

</td>

<td class="new_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1162" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">custom_old</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

</td>

<td class="new_line diff-line-num" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1163" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1158

</td>

<td class="new_line diff-line-num" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1164

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1164" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using Custom Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1159

</td>

<td class="new_line diff-line-num" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1165

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1165" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1160

</td>

<td class="new_line diff-line-num" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1166" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1161" 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">

1161

</td>

<td class="new_line diff-line-num old" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1161" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1167

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1167" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

</td>

<td class="new_line diff-line-num" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1168" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">custom_new</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="new_line diff-line-num" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1169

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1169" class="line" lang="cpp">      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CustomGeometry</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aopt</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1164

</td>

<td class="new_line diff-line-num" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1170

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1170" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->warn("Using Custom Setting for Alevin");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1165

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<td class="new_line diff-line-num" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1171

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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="cpp">      <span class="n" style="color: #333;">initiatePipeline</span><span class="p">(</span><span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

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<td class="new_line diff-line-num" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1172

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1172" class="line" lang="cpp">                       <span class="n" style="color: #333;">vm</span><span class="p">,</span> <span class="n" style="color: #333;">commentString</span><span class="p">,</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1167" 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">

1167

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<td class="new_line diff-line-num old" data-linenumber="1173" 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="LC1167" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1173

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1173" class="line" lang="cpp">                       <span class="n" style="color: #333;">barcodeFiles</span><span class="p">,</span> <span class="n" style="color: #333;">readFiles</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1168

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<td class="new_line diff-line-num" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1174

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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1169

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<td class="new_line diff-line-num" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1175

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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1170

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<td class="new_line diff-line-num" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1176

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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">error</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>

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<br>

</li>

<li id="9fcb6347f66e2015a27d89eec62944e82352b5d9">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#9fcb6347f66e2015a27d89eec62944e82352b5d9"><strong>src/AlevinHash.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" style="width: 35px; color: rgba(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="294" style="width: 35px; color: rgba(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">@@ -294,7 +294,7 @@ int salmonHashQuantify(AlevinOpts<apt::CITESeq>& aopt,</td>

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294

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">                       <span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outputDirectory</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(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="LC295" class="line" lang="cpp">                       <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(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="LC296" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="297" 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="LC297" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonHashQuantify</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(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="LC297" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonHashQuantify</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp">                       <span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outputDirectory</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(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="LC299" class="line" lang="cpp">                       <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(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="LC300" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" style="width: 35px; color: rgba(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="310" style="width: 35px; color: rgba(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">@@ -310,6 +310,10 @@ int salmonHashQuantify(AlevinOpts<apt::QuartzSeq2>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="cpp">                       <span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outputDirectory</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp">                       <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonHashQuantify</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">                       <span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outputDirectory</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">                       <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonHashQuantify</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp">                       <span class="n" style="color: #333;">bfs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outputDirectory</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="cpp">                       <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">);</span></span>

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<br>

</li>

<li id="d95dc025bfe71cabe95139b51ea263244f8cbab2">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#d95dc025bfe71cabe95139b51ea263244f8cbab2"><strong>src/AlevinUtils.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(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="101" style="width: 35px; color: rgba(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">@@ -101,6 +101,14 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(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="LC104" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">getReadSequence</span><span class="p">(</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">protocol</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(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="LC105" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(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="LC107" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">subseq</span><span class="p">){</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(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="LC108" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(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="LC109" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq2</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(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="LC110" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(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="LC111" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">getReadSequence</span><span class="p">(</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">protocol</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(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="LC113" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(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="LC114" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(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="134" style="width: 35px; color: rgba(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">@@ -126,12 +134,12 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(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="LC136" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="137" 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="LC129" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">getReadSequence</span><span class="p">(</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">protocol</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span>  <span class="n" style="color: #333;">getReadSequence</span><span class="p">(</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">protocol</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="139" style="width: 35px; color: rgba(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="LC139" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="140" style="width: 35px; color: rgba(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="LC140" class="line" lang="cpp">                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">subseq</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="141" 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="LC133" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="134" 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="LC134" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq<span class="idiff left right">2</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">seq<span class="idiff left right">2</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// end of read extraction</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></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">@@ -223,6 +231,16 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">        <span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractUMI</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">                                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">                                     <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(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="LC237" class="line" lang="cpp">                                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">umi</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">read2</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span> <span class="o" style="font-weight: 600;">&&</span> </span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">        <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="c1" style="color: #998; font-style: italic;">// for the rare case if barcode has one N and thus gets recovered</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp">          <span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorSeqLen</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractUMI</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">                                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">                                 <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</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">@@ -233,14 +251,14 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractUMI</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractUMI</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp">                                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp">                                 <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">                                 <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp">                                 <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">umi</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">read</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="cpp">      <span class="p"><span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="259" 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="LC242" class="line" lang="cpp">      <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">cout</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Incorrect call for umi extract"</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp">      <span class="n" style="color: #333;"><span class="idiff left">exit</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(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="LC259" class="line" lang="cpp">      <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">w1Length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">barcodeLength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">umiLength</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">?</span></span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">      <span class="idiff left">  </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">umi</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assign</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bc2EndPos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">umiLength</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(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="LC261" class="line" lang="cpp">      <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="244" style="width: 35px; color: rgba(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="LC262" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="246" style="width: 35px; color: rgba(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="LC264" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" style="width: 35px; color: rgba(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="307" style="width: 35px; color: rgba(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">@@ -289,6 +307,27 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp">        <span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractBarcode</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(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="LC311" class="line" lang="cpp">                                         <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(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="LC312" class="line" lang="cpp">                                          <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">                                          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">read2</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">      <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorSeq</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(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="LC316" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">maxHairpinIndexLen</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">maxHairpinIndexLen</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// only 2 possible values of pt.anchorPos</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">         <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorSeqLen</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">           <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">bcAssign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorSeqLen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">rtIdxLen</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">anchorPos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">maxHairpinIndexLen</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// hairpin index can be 9 or 10 bp</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">           <span class="n" style="color: #333;">bcAssign</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"AC"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">          <span class="n" style="color: #333;">bcAssign</span> <span class="o" style="font-weight: 600;">+=</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="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(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="LC324" class="line" lang="cpp">        <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">bcAssign</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(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="LC325" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractBarcode</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp">                                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="333" style="width: 35px; color: rgba(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="LC333" class="line" lang="cpp">                                     <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="339" style="width: 35px; color: rgba(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="378" style="width: 35px; color: rgba(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">@@ -339,21 +378,49 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp">        <span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="p">></span></span>

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<td class="new_line diff-line-num old" data-linenumber="381" 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="LC342" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractBarcode</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> </span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extractBarcode</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> </span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp">                                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> </span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp">                                     <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">read2</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">size_type</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">index</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span><span class="p">){</span></span>

</pre>

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348

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<td class="new_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp">                                     <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDropV2</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="n" style="color: #333;">read</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">umiLength</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">      <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read2</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(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="LC387" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">npos</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(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="LC389" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(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="LC390" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hammingDistance</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Length</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">maxHammingDist</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(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="LC391" class="line" lang="cpp">            <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(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="LC392" class="line" lang="cpp">            <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(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="LC393" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(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="LC394" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<span id="LC396" 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;">found</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;}</span></span>

</pre>

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349

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397

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="350" 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">

350

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<td class="new_line diff-line-num old" data-linenumber="398" 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="LC350" class="line" lang="cpp">      <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="351" 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">

351

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<td class="new_line diff-line-num old" data-linenumber="398" 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="LC351" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">8</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">12</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">8</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">11</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

352

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<td class="new_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

399

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

353

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<td class="new_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

400

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp">      <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read2</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1Pos</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

354

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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

402

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">w1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="355" 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">

355

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<td class="new_line diff-line-num old" data-linenumber="403" 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="LC355" class="line" lang="cpp">      <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp">      <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read2</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bc2Len</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">barcodeLength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp">      <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp">        <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"A"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

410

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp">        <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"AT"</span><span class="p">;</span></span>

</pre>

</td>

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411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

412

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

413

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp">        <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"AAG"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

416

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp">        <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"AAAC"</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp">      <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bc2EndPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bc2Len</span><span class="p">;</span></span>

</pre>

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356

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<td class="new_line diff-line-num" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

420

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

422

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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424

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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358

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<td class="new_line diff-line-num" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

425

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"></span>

</pre>

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359

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<td class="new_line diff-line-num" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

426

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getIndelNeighbors</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="437" style="width: 35px; color: rgba(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="504" style="width: 35px; color: rgba(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">@@ -437,6 +504,16 @@ namespace alevin {</td>

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437

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504

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp">                        <span class="n" style="color: #333;">neighbors</span><span class="p">);</span></span>

</pre>

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438

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505

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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439

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<td class="new_line diff-line-num" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(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="LC507" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hammingDistance</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s2</span><span class="p">){</span></span>

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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(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="LC508" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">s2</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"Strings have different lengths, can't compute hamming distance"</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(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="LC510" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// compute dot product for all postisions, start with 0 and add if the values are not equal</span></span>

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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(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="LC513" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">inner_product</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">s1</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span><span class="n" style="color: #333;">s2</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">plus</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">not2</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">equal_to</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;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span><span class="o" style="font-weight: 600;">></span><span class="p">()));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getTxpToGeneMap</span><span class="p">(</span><span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp">                         <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp">                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t2gFileName</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1351" style="width: 35px; color: rgba(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">@@ -1274,7 +1351,7 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cpp">                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

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<td class="new_line diff-line-num" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1353

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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1277" 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">

1277

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<td class="new_line diff-line-num old" data-linenumber="1354" 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="LC1277" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1278" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1354

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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1278

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<td class="new_line diff-line-num" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1355

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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1279

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<td class="new_line diff-line-num" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1356

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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp">                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

</pre>

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1280

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<td class="new_line diff-line-num" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1357

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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1306" style="width: 35px; color: rgba(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="1383" style="width: 35px; color: rgba(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">@@ -1306,6 +1383,10 @@ namespace alevin {</td>

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<td class="old_line diff-line-num" data-linenumber="1306" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1383" style="width: 35px; color: rgba(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="LC1383" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1307

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<td class="new_line diff-line-num" data-linenumber="1384" style="width: 35px; color: rgba(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="LC1384" class="line" lang="cpp">                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

</pre>

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1308

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<td class="new_line diff-line-num" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1385

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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1386" style="width: 35px; color: rgba(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="LC1386" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1387" style="width: 35px; color: rgba(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="LC1387" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1388" class="line" lang="cpp">                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1389

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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1309

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<td class="new_line diff-line-num" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1390

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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">processAlevinOpts</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1310" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1391

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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="cpp">                           <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noTgMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1311

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<td class="new_line diff-line-num" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1392

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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="cpp">                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="2d5e0752f505025e2570ff24aee737c61f0ebcdd">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#2d5e0752f505025e2570ff24aee737c61f0ebcdd"><strong>src/BuildSalmonIndex.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">@@ -43,7 +43,7 @@</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// http://stackoverflow.com/questions/108318/whats-the-simplest-way-to-test-whether-a-number-is-a-power-of-2-in-c</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isPowerOfTwo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">and</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonIndex</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonIndex</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* salmonIndex */</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">bfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="256" style="width: 35px; color: rgba(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="256" style="width: 35px; color: rgba(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">@@ -256,3 +256,25 @@ Creates a salmon index.</td>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(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="LC260" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">checkLoadIndex</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">spdlog</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// ==== Figure out the index type</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">  <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">versionPath</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <span class="n" style="color: #333;">indexDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"versionInfo.json"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">  <span class="n" style="color: #333;">SalmonIndexVersionInfo</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(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="LC265" class="line" lang="cpp">  <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">versionPath</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexVersion</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">    <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MemoryWriter</span> <span class="n" style="color: #333;">infostr</span><span class="p">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="cpp">    <span class="n" style="color: #333;">infostr</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(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="LC269" class="line" lang="cpp">      <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: The index version file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">versionPath</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(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="LC270" class="line" lang="cpp">      <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" doesn't seem to exist.  Please try re-building the salmon "</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">      <span class="s" style="color: #d14;">"index."</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span><span class="n" style="color: #333;">infostr</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">());</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(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="LC273" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Check index version compatibility here</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">indexType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(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="LC276" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// ==== Figure out the index type</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(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="LC277" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">res</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SalmonIndex</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">indexType</span><span class="p">));</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(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="LC278" class="line" lang="cpp">  <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">indexDirectory</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="4d255e86e1e69399b0a00c7213bf7ae26df399d4">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#4d255e86e1e69399b0a00c7213bf7ae26df399d4"><strong>src/CollapsedCellOptimizer.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1438" style="width: 35px; color: rgba(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="1438" style="width: 35px; color: rgba(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">@@ -1438,7 +1438,7 @@ template</td>

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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CollapsedCellOptimizer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize</span><span class="p">(</span><span class="n" style="color: #333;">EqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fullEqMap</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="1439" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1439" style="width: 35px; color: rgba(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="LC1439" class="line" lang="cpp">                                      <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1440" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1440

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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="cpp">                                      <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1441" 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">

1441

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<td class="new_line diff-line-num old" data-linenumber="1441" 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="LC1441" class="line" lang="cpp">                                      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1442" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1441

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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="cpp">                                      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1442

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<td class="new_line diff-line-num" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1442

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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp">                                      <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gzw</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1443

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<td class="new_line diff-line-num" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1443

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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">umiCount</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1516,6 +1516,16 @@ bool CollapsedCellOptimizer::optimize(EqMapT& fullEqMap,</td>

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<td class="old_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="cpp">                                      <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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1518

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<pre style="margin: 0;"> <span id="LC1518" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CollapsedCellOptimizer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize</span><span class="p">(</span><span class="n" style="color: #333;">EqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fullEqMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1521

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1521" class="line" lang="cpp">                                      <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1522

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1522" class="line" lang="cpp">                                      <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1523

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1523" class="line" lang="cpp">                                      <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1524

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1524" class="line" lang="cpp">                                      <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gzw</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1525

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1525" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1526

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1526" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">umiCount</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1527

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1527" class="line" lang="cpp">                                      <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1528

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1528" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1519

</td>

<td class="new_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1529" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1520

</td>

<td class="new_line diff-line-num" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1530

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1521

</td>

<td class="new_line diff-line-num" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1531

</td>

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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CollapsedCellOptimizer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize</span><span class="p">(</span><span class="n" style="color: #333;">EqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fullEqMap</span><span class="p">,</span></span>

</pre>

</td>

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<br>

</li>

<li id="3bcd26cb8cf945e15663285c1e7eeb25ccc7e9be">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#3bcd26cb8cf945e15663285c1e7eeb25ccc7e9be"><strong>src/GZipWriter.cpp</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1865,8 +1865,8 @@ bool GZipWriter::writeEquivCounts<SCExpT, apt::CITESeq>(</td>

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<td class="old_line diff-line-num" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1865

</td>

<td class="new_line diff-line-num" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1865

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<pre style="margin: 0;"> <span id="LC1865" class="line" lang="cpp">                                                        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1866

</td>

<td class="new_line diff-line-num" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1866

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1866" class="line" lang="cpp">                                                        <span class="n" style="color: #333;">SCExpT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readExp</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1867

</td>

<td class="new_line diff-line-num" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1867

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1867" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1868" 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">

1868

</td>

<td class="new_line diff-line-num old" data-linenumber="1868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1868" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeEquivCounts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SCExpT</span><span class="p">,</span> <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="p">>(</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1869" 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">

1869

</td>

<td class="new_line diff-line-num old" data-linenumber="1868" 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="LC1869" class="line" lang="cpp">                                                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1870" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1868

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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeEquivCounts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SCExpT</span><span class="p">,</span> <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="p">>(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1869

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1869" class="line" lang="cpp">                                                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1870

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<td class="new_line diff-line-num" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1870

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<pre style="margin: 0;"> <span id="LC1870" class="line" lang="cpp">                                                       <span class="n" style="color: #333;">SCExpT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readExp</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1871

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<td class="new_line diff-line-num" data-linenumber="1871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1871

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<pre style="margin: 0;"> <span id="LC1871" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1872

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<td class="new_line diff-line-num" data-linenumber="1872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1872

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<pre style="margin: 0;"> <span id="LC1872" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeEquivCounts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SCExpT</span><span class="p">,</span> <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChromiumV3</span><span class="p">>(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1893" style="width: 35px; color: rgba(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="1893" style="width: 35px; color: rgba(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">@@ -1893,6 +1893,10 @@ bool GZipWriter::writeEquivCounts<SCExpT, apt::QuartzSeq2>(</td>

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<td class="old_line diff-line-num" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1893

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<td class="new_line diff-line-num" data-linenumber="1893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1893

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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="cpp">                                                        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1894

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<td class="new_line diff-line-num" data-linenumber="1894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1894

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<pre style="margin: 0;"> <span id="LC1894" class="line" lang="cpp">                                                        <span class="n" style="color: #333;">SCExpT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readExp</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1895

</td>

<td class="new_line diff-line-num" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1895

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1895" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1896" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1896

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<pre style="margin: 0;">+<span id="LC1896" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeEquivCounts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SCExpT</span><span class="p">,</span> <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="p">>(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1897

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<pre style="margin: 0;">+<span id="LC1897" class="line" lang="cpp">                                                         <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1898

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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="cpp">                                                         <span class="n" style="color: #333;">SCExpT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readExp</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1899

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1899" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1896

</td>

<td class="new_line diff-line-num" data-linenumber="1900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1900

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1900" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeEquivCounts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SCExpT</span><span class="p">,</span> <span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="p">>(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1897

</td>

<td class="new_line diff-line-num" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1901

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<pre style="margin: 0;"> <span id="LC1901" class="line" lang="cpp">                                                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1898

</td>

<td class="new_line diff-line-num" data-linenumber="1902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1902

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1902" class="line" lang="cpp">                                                       <span class="n" style="color: #333;">SCExpT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readExp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1907" style="width: 35px; color: rgba(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="1911" style="width: 35px; color: rgba(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">@@ -1907,7 +1911,7 @@ template bool</td>

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<td class="old_line diff-line-num" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1907

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<td class="new_line diff-line-num" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1911

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<pre style="margin: 0;"> <span id="LC1911" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1908

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<td class="new_line diff-line-num" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

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<pre style="margin: 0;"> <span id="LC1912" class="line" lang="cpp">                                          <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">aux_dir</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1909

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<td class="new_line diff-line-num" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

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<pre style="margin: 0;"> <span id="LC1913" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1910" 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">

1910

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<td class="new_line diff-line-num old" data-linenumber="1914" 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="LC1910" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1914

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<pre style="margin: 0;">+<span id="LC1914" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left">V2</span></span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff right">V2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1911

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<td class="new_line diff-line-num" data-linenumber="1915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1915

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<pre style="margin: 0;"> <span id="LC1915" class="line" lang="cpp">                                         <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">aux_dir</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1912

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<td class="new_line diff-line-num" data-linenumber="1916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1916

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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1913

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<td class="new_line diff-line-num" data-linenumber="1917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1917

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<pre style="margin: 0;"> <span id="LC1917" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1925,6 +1929,9 @@ template bool</td>

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<td class="old_line diff-line-num" data-linenumber="1925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1925

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<td class="new_line diff-line-num" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1929

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<pre style="margin: 0;"> <span id="LC1929" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1926

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<td class="new_line diff-line-num" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1930

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<pre style="margin: 0;"> <span id="LC1930" class="line" lang="cpp">                                             <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">aux_dir</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1927

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<td class="new_line diff-line-num" data-linenumber="1931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1931

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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1932

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1932" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1933

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<pre style="margin: 0;">+<span id="LC1933" class="line" lang="cpp">                                           <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">aux_dir</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1934

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<pre style="margin: 0;">+<span id="LC1934" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1928

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<td class="new_line diff-line-num" data-linenumber="1935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1935

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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="cpp"><span class="n" style="color: #333;">GZipWriter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeMetaAlevin</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="p">>(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">opts</span><span class="p">,</span></span>

</pre>

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1929

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<td class="new_line diff-line-num" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1936

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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="cpp">                                         <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">aux_dir</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1930

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1937

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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<br>

</li>

<li id="f172e578ce4bd88dde4a1e5db8b0748de9bb9a18">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#f172e578ce4bd88dde4a1e5db8b0748de9bb9a18"><strong>src/ProgramOptionsGenerator.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="335" style="width: 35px; color: rgba(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="335" style="width: 35px; color: rgba(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">@@ -335,8 +335,8 @@ namespace salmon {</td>

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335

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335

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp">                                       <span class="s" style="color: #d14;">"alevin-developer Options"</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

336

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336

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp">    <span class="n" style="color: #333;">alevindevs</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

337

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337

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp">      <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="338" 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">

338

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<td class="new_line diff-line-num old" data-linenumber="338" 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="LC338" class="line" lang="cpp">       <span class="s" style="color: #d14;">"indrop"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bool_switch</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaults</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isInDrop</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="339" 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">

339

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<td class="new_line diff-line-num old" data-linenumber="338" 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="LC339" class="line" lang="cpp">       <span class="s" style="color: #d14;">"Use inDrop<span class="idiff left"> (not extensively tested)</span> Single Cell protocol for the library. <span class="idiff right">m</span>ust specify w1 too."</span><span class="p">)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

338

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">       <span class="s" style="color: #d14;">"indrop<span class="idiff left right">V2</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bool_switch</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaults</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isInDrop</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

339

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">       <span class="s" style="color: #d14;">"Use inDrop<span class="idiff left">V2</span> Single Cell protocol for the library. <span class="idiff right">M</span>ust specify w1 too."</span><span class="p">)</span></span>

</pre>

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340

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<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

340

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp">      <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

341

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<td class="new_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(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="LC341" class="line" lang="cpp">       <span class="s" style="color: #d14;">"w1"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value</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;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(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="LC342" class="line" lang="cpp">       <span class="s" style="color: #d14;">"Must be used in conjunction with inDrop;"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="413" style="width: 35px; color: rgba(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="413" style="width: 35px; color: rgba(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">@@ -413,6 +413,9 @@ namespace salmon {</td>

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413

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413

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp">      <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp">       <span class="s" style="color: #d14;">"quartzseq2"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bool_switch</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaults</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isQuartzSeq2</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp">       <span class="s" style="color: #d14;">"Use Quartz-Seq2 v3.2 Single Cell protocol for the library assumes 15 length barcode and 8 length UMI."</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp">      <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp">       <span class="s" style="color: #d14;">"sciseq3"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bool_switch</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaults</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isSciSeq3</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp">       <span class="s" style="color: #d14;">"Use sci-RNA-seq3 protocol for the library."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp">      <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp">       <span class="s" style="color: #d14;">"whitelist"</span><span class="p">,</span> <span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value</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;">string</span><span class="o" style="font-weight: 600;">></span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp">       <span class="s" style="color: #d14;">"File containing white-list barcodes"</span><span class="p">)</span></span>

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<br>

</li>

<li id="56c25523d0e5423ba1e491804ea1df82bdaf152b">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#56c25523d0e5423ba1e491804ea1df82bdaf152b"><strong>src/Salmon.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GenomicFeature.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonConfig.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "VersionChecker.hpp"</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonIndex.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="cm" style="color: #998; font-style: italic;">/*opts*/</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">help</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="cm" style="color: #998; font-style: italic;">/*opts*/</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">  <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">MemoryWriter</span> <span class="n" style="color: #333;">helpMsg</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">  <span class="n" style="color: #333;">helpMsg</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"salmon v{}</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">salmon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">  <span class="n" style="color: #333;">helpMsg</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(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="91" style="width: 35px; color: rgba(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">@@ -90,10 +91,12 @@ int dualModeMessage() {</td>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">SubCmdType</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Bonus!</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonSwim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="cm" style="color: #998; font-style: italic;">/*argc*/</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="cm" style="color: #998; font-style: italic;">/*argv*/</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonSwim</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="cm" style="color: #998; font-style: italic;">/*argc*/</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="cm" style="color: #998; font-style: italic;">/*argv*/</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/*index*/</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">R"(</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="s" style="color: #d14;">    _____       __</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,17 +147,18 @@ bibtex:</td>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="s" style="color: #d14;">)"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="150" 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="LC147" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonIndex</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="150" 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="LC148" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="150" 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="LC149" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(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="LC150" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonIndex</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(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="LC151" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentDualMode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// TODO : PF_INTEGRATION</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="155" 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="LC151" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonBarcoding</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="155" 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="LC152" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantMerge</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(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="LC155" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonBarcoding</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(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="LC156" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantMerge</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp">                     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp">  <span class="n" style="color: #333;">show_backtrace</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setlocale</span><span class="p">(</span><span class="n" style="color: #333;">LC_ALL</span><span class="p">,</span> <span class="s" style="color: #d14;">"en_US.UTF-8"</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="235" style="width: 35px; color: rgba(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="239" style="width: 35px; color: rgba(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">@@ -235,9 +239,9 @@ int main(int argc, char* argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">      <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="242" 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="LC238" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">function</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[])</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">></span>></span> <span class="n" style="color: #333;">cmds</span><span class="p">(</span></span>

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<td class="old_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(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="LC242" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">SubCmdType</span></span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cmds</span><span class="p">(</span></span>

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<td class="new_line diff-line-num" data-linenumber="243" style="width: 35px; color: rgba(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="LC243" class="line" lang="cpp">        <span class="p">{{</span><span class="s" style="color: #d14;">"index"</span><span class="p">,</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">},</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp">         <span class="p">{</span><span class="s" style="color: #d14;">"quant"</span><span class="p">,</span> <span class="n" style="color: #333;">salmon<span class="idiff left right">Quantify</span></span><span class="p">},</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">         <span class="p">{</span><span class="s" style="color: #d14;">"quant"</span><span class="p">,</span> <span class="n" style="color: #333;">salmon<span class="idiff left right">AlignmentDualMode</span></span><span class="p">},</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp">         <span class="p">{</span><span class="s" style="color: #d14;">"quantmerge"</span><span class="p">,</span> <span class="n" style="color: #333;">salmonQuantMerge</span><span class="p">},</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp">         <span class="c1" style="color: #998; font-style: italic;">// TODO : PF_INTEGRATION</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">         <span class="p">{</span><span class="s" style="color: #d14;">"alevin"</span><span class="p">,</span> <span class="n" style="color: #333;">salmonBarcoding</span><span class="p">},</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" style="width: 35px; color: rgba(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="255" style="width: 35px; color: rgba(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">@@ -251,64 +255,24 @@ int main(int argc, char* argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    std::copy_n( &argv[topLevelArgc], argc-topLevelArgc, &argv2[1] );</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    */</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">subCommandArgc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="258" 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="LC255" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="p">[]</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">argv2</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">subCommandArgc</span><span class="p">]);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(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="LC258" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">preloadedIndex</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(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="LC259" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(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="LC260" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nargc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(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="LC261" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="p">[]</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">argv2</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">nargc</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp">    <span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;"><span class="idiff left right">subCommandA</span>rgc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;"><span class="idiff left right">na</span>rgc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp">      <span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>

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<td class="old_line diff-line-num" data-linenumber="259" style="width: 35px; color: rgba(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="LC265" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">nargv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv2</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">();</span></span>

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<td class="new_line diff-line-num" data-linenumber="267" style="width: 35px; color: rgba(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="LC267" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC261" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cmdMain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmds</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC262" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmdMain</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cmds</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// help(subCommandArgc, argv2);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="264" 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="LC264" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">help</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// If the command is quant; determine whether</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// we're quantifying with raw sequences or alignments</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmdMain</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"quant"</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC269" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="270" 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="LC270" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">subCommandArgc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="271" 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="LC271" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dualModeMessage</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="272" 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="LC272" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// detect mode-specific help request</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC274" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help-alignment"</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="275" 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">

275

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC275" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">helpStr</span><span class="p">{</span><span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="276" 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">

276

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">helpStr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]};</span></span>

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<td class="old_line diff-line-num old" data-linenumber="277" 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">

277

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC277" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonAlignmentQuantify</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="278" 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">

278

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC278" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help-reads"</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="279" 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">

279

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC279" class="line" lang="cpp">          <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">helpStr</span><span class="p">{</span><span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'p'</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">};</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC280" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">helpStr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]};</span></span>

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<td class="old_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC281" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonQuantify</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC282" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC283" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC284" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// detect general help request</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC285" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC286" class="line" lang="cpp">            <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC287" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dualModeMessage</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="289" 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="LC289" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="290" 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="LC290" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// otherwise, detect and dispatch the correct mode</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useSalmonAlign</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC292" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;">subCommandArgc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="293" 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="LC293" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp">              <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp">              <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"--alignments"</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp">              <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"--eqclasses"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

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<td class="old_line diff-line-num old" data-linenumber="297" 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="LC297" class="line" lang="cpp">              <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"--ont"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp">            <span class="n" style="color: #333;">useSalmonAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp">          <span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="301" 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="LC301" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="old_line diff-line-num old" data-linenumber="302" 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="LC302" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useSalmonAlign</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="303" 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="LC303" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonAlignmentQuantify</span><span class="p">(</span><span class="n" style="color: #333;">subCommandArgc</span><span class="p">,</span> <span class="n" style="color: #333;">argv2</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>

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<td class="old_line diff-line-num old" data-linenumber="304" 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="LC304" class="line" lang="cpp">        <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="LC305" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonQuantify</span><span class="p">(</span><span class="n" style="color: #333;">subCommandArgc</span><span class="p">,</span> <span class="n" style="color: #333;">argv2</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cmdMain</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">(</span><span class="n" style="color: #333;">subCommandArgc</span><span class="p">,</span> <span class="n" style="color: #333;">argv2</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(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="LC269" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">cmdMain</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmds</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(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="LC270" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmdMain</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cmds</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(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="LC271" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// help(subCommandArgc, argv2);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(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="LC272" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">help</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cmdMain</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">(</span><span class="n" style="color: #333;">nargc</span><span class="p">,</span> <span class="n" style="color: #333;">nargv</span><span class="p">,</span> <span class="n" style="color: #333;">preloadedIndex</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(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="LC275" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="276" 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="LC311" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">po</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">error</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" 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="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Program Option Error (main) : ["</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="278" style="width: 35px; color: rgba(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="LC278" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"].</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Exiting.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,3 +285,41 @@ int main(int argc, char* argv[]) {</td>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentDualMode</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[],</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// If the command is quant; determine whether</span></span>

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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// we're quantifying with raw sequences or alignments</span></span>

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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dualModeMessage</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// detect mode-specific help request</span></span>

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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(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="LC296" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help-alignment"</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(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="LC297" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(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="LC298" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonAlignmentQuantify</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(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="LC299" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help-reads"</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">};</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonQuantify</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">helpArgv</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// detect general help request</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dualModeMessage</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(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="LC309" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// otherwise, detect and dispatch the correct mode</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useSalmonAlign</span><span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(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="LC311" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;">argc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(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="LC312" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(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="LC313" class="line" lang="cpp">        <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(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="LC314" class="line" lang="cpp">        <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"--alignments"</span><span class="p">,</span> <span class="mi" style="color: #099;">12</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">or</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(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="LC315" class="line" lang="cpp">        <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"--eqclasses"</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(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="LC316" class="line" lang="cpp">      <span class="n" style="color: #333;">useSalmonAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(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="LC317" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useSalmonAlign</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(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="LC321" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonAlignmentQuantify</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">salmonQuantify</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="f6eb2d02fae3bac60ea268026fe2765f446b2a4d">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#f6eb2d02fae3bac60ea268026fe2765f446b2a4d"><strong>src/SalmonAlevin.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <functional></span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iterator></span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <map></span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <mutex></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -633,6 +634,7 @@ void process_reads_sc_sketch(paired_parser* parser, ReadExperimentT& readExp, Re</td>

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="cpp">          <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">reserveSize</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">localProtocol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;">rangeSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// For all the read in this batch</span></span>

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp">      <span class="n" style="color: #333;">readLenLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="661" style="width: 35px; color: rgba(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="663" style="width: 35px; color: rgba(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">@@ -661,7 +663,7 @@ void process_reads_sc_sketch(paired_parser* parser, ReadExperimentT& readExp, Re</td>

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661

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//barcode.clear();</span></span>

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp">      <span class="n" style="color: #333;">nonstd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodeIdx</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp">      <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>

</pre>

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665

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// keep track of the *least* freqeuntly </span></span>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// occurring hit in this fragment to consider </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="671" style="width: 35px; color: rgba(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="673" style="width: 35px; color: rgba(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">@@ -671,19 +673,30 @@ void process_reads_sc_sketch(paired_parser* parser, ReadExperimentT& readExp, Re</td>

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp">          <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">THREE</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp">        <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_bc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span></span>

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp">          <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC677" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC679" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recovered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC680" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recovered</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If the barcode sequence could be extracted, then this is set to true,</span></span>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// but the barcode sequence itself may still be invalid (e.g. contain `N` characters).</span></span>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// However, if extracted_barcode is false here, there is no hope to even recover the</span></span>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// barcode and we shouldn't attempt it.</span></span>

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">localProtocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we could pull out something where the barcode sequence should have been</span></span>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// then continue to process it.</span></span>

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_barcode</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// if the barcode consisted of valid nucleotides, then seqOk is true</span></span>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// otherwise false</span></span>

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp">          <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If the barcode contained invalid nucleotides</span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// this attempts to replace the first one with an `A`.</span></span>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If this returns true, there was only one `N` and we</span></span>

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// replaced it; otherwise there was more than one `N`</span></span>

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// and the barcode sequence should be treated as invalid.</span></span>

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp">            <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we have a valid barcode</span></span>

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqOk</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC686" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//aopt.jointLog->info("BC : {}, UMI : {}". barcode, umi);</span></span>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">localProtocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC700" 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;">umi_ok</span> <span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC701" class="line" lang="cpp">            <span class="n" style="color: #333;">smallSeqs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

689

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<td class="new_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp">          <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1162" style="width: 35px; color: rgba(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="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1162,6 +1175,7 @@ void process_reads_sc_align(paired_parser* parser, ReadExperimentT& readExp, Rea</td>

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<td class="old_line diff-line-num" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

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<td class="new_line diff-line-num" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1175

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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="cpp">         <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">reserveSize</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1163

</td>

<td class="new_line diff-line-num" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1176

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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1164

</td>

<td class="new_line diff-line-num" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1177

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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1178

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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">localProtocol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1165

</td>

<td class="new_line diff-line-num" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1179

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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;">rangeSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// For all the read in this batch</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

</td>

<td class="new_line diff-line-num" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1180

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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

</td>

<td class="new_line diff-line-num" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1181

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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp">      <span class="n" style="color: #333;">readLenLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1188,23 +1202,34 @@ void process_reads_sc_align(paired_parser* parser, ReadExperimentT& readExp, Rea</td>

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<td class="old_line diff-line-num" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1188

</td>

<td class="new_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//barcode.clear();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1189

</td>

<td class="new_line diff-line-num" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cpp">      <span class="n" style="color: #333;">nonstd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodeIdx</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1190

</td>

<td class="new_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

</td>

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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cpp">      <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1191" 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">

1191

</td>

<td class="new_line diff-line-num old" data-linenumber="1205" 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="LC1191" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1205

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1192

</td>

<td class="new_line diff-line-num" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1193

</td>

<td class="new_line diff-line-num" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1207

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1207" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1194

</td>

<td class="new_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="cpp">          <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">THREE</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1195" 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">

1195

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1195" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1196" 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">

1196

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1196" class="line" lang="cpp">        <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_barcode</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1197" 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">

1197

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1197" class="line" lang="cpp">          <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1198" 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">

1198

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1198" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1199" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1200" 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">

1200

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1200" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recovered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1201" 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">

1201

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<td class="new_line diff-line-num old" data-linenumber="1209" 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="LC1201" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recovered</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1209" style="width: 35px; color: rgba(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="LC1209" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If the barcode sequence could be extracted, then this is set to true,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1210" style="width: 35px; color: rgba(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="LC1210" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// but the barcode sequence itself may still be invalid (e.g. contain `N` characters).</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1211

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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// However, if extracted_barcode is false here, there is no hope to even recover the</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1212

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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// barcode and we shouldn't attempt it.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1213

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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">localProtocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1214

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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we could pull out something where the barcode sequence should have been</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1215

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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// then continue to process it.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1216

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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_barcode</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1217

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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// if the barcode consisted of valid nucleotides, then seqOk is true</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1218

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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// otherwise false</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1219

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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="cpp">          <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1220

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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1221

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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If the barcode contained invalid nucleotides</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1222

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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// this attempts to replace the first one with an `A`.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1223

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1223" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If this returns true, there was only one `N` and we</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1224

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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// replaced it; otherwise there was more than one `N`</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1225

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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// and the barcode sequence should be treated as invalid.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1226

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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="cpp">            <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1227

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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

</td>

<td class="new_line diff-line-num" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1228

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

</td>

<td class="new_line diff-line-num" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1229

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1229" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

</td>

<td class="new_line diff-line-num" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1230

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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we have a valid barcode</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

</td>

<td class="new_line diff-line-num" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1231

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1231" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqOk</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1206" 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">

1206

</td>

<td class="new_line diff-line-num old" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1206" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1207" 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">

1207

</td>

<td class="new_line diff-line-num old" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1207" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1232

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">localProtocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1208

</td>

<td class="new_line diff-line-num" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1233

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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="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;">umi_ok</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1209

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<td class="new_line diff-line-num" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1234

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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="cpp">            <span class="n" style="color: #333;">smallSeqs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1210

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<td class="new_line diff-line-num" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1235

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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="cpp">          <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1384" style="width: 35px; color: rgba(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="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1384,7 +1409,7 @@ void process_reads_sc_align(paired_parser* parser, ReadExperimentT& readExp, Rea</td>

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<td class="old_line diff-line-num" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1384

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<td class="new_line diff-line-num" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1409

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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1385

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<td class="new_line diff-line-num" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1410

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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcode_ok</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1386

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<td class="new_line diff-line-num" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1411

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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp">            <span class="n" style="color: #333;">unmapped_bc_map</span><span class="p">[</span><span class="n" style="color: #333;">bck</span><span class="p">.</span><span class="n" style="color: #333;">word</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1387" 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">

1387

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<td class="new_line diff-line-num old" data-linenumber="1412" 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="LC1387" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1412" style="width: 35px; color: rgba(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="LC1412" class="line" lang="cpp">          <span class="p">}</span><span class="idiff left right"> </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1388

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<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1413

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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1389

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<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1414

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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1390

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<td class="new_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1415

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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1644" style="width: 35px; color: rgba(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">@@ -1619,6 +1644,7 @@ void processReadsQuasi(</td>

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<td class="old_line diff-line-num" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1619

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<td class="new_line diff-line-num" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1644

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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="cpp">         <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">reserveSize</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1620

</td>

<td class="new_line diff-line-num" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1645

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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1621

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<td class="new_line diff-line-num" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1646

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1646" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1647

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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">localProtocol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1622

</td>

<td class="new_line diff-line-num" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1648

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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" 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;">rangeSize</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// For all the read in this batch</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1623

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<td class="new_line diff-line-num" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1649

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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1624

</td>

<td class="new_line diff-line-num" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1650

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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="cpp">      <span class="n" style="color: #333;">readLenLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1646" style="width: 35px; color: rgba(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="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1646,17 +1672,29 @@ void processReadsQuasi(</td>

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<td class="old_line diff-line-num" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1646

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<td class="new_line diff-line-num" data-linenumber="1672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1672

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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//barcode.clear();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1647

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<td class="new_line diff-line-num" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1673

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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="cpp">      <span class="n" style="color: #333;">nonstd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optional</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodeIdx</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1648

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<td class="new_line diff-line-num" data-linenumber="1674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1674

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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="cpp">      <span class="n" style="color: #333;">extraBAMtags</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1649" 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">

1649

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<td class="new_line diff-line-num old" data-linenumber="1675" 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="LC1649" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1675" style="width: 35px; color: rgba(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="LC1675" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">seqOk</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1650

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<td class="new_line diff-line-num" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1676

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<pre style="margin: 0;"> <span id="LC1676" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1651

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<td class="new_line diff-line-num" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1677

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<pre style="margin: 0;"> <span id="LC1677" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FIVE</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1652

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<td class="new_line diff-line-num" data-linenumber="1678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1678

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<pre style="margin: 0;"> <span id="LC1678" class="line" lang="cpp">          <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcEnd</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">THREE</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1653" 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">

1653

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1653" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">alevinOpts</span><span class="p">.</span><span class="n" style="color: #333;">protocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1654" 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">

1654

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1654" class="line" lang="cpp">        <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_barcode</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1655" 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">

1655

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1655" class="line" lang="cpp">          <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1656" 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">

1656

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1656" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1657" 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">

1657

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1657" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1658" 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">

1658

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1658" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recovered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1659" 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">

1659

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<td class="new_line diff-line-num old" data-linenumber="1679" 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="LC1659" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recovered</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If the barcode sequence could be extracted, then this is set to true,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1680" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// but the barcode sequence itself may still be invalid (e.g. contain `N` characters).</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1681" style="width: 35px; color: rgba(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="LC1681" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// However, if extracted_barcode is false here, there is no hope to even recover the</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1682" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// barcode and we shouldn't attempt it.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">extracted_barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractBarcode</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">localProtocol</span><span class="p">,</span> <span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1684" style="width: 35px; color: rgba(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="LC1684" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we could pull out something where the barcode sequence should have been</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1685" style="width: 35px; color: rgba(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="LC1685" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// then continue to process it.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1686" style="width: 35px; color: rgba(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="LC1686" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extracted_barcode</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1687" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// if the barcode consisted of valid nucleotides, then seqOk is true</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1688" style="width: 35px; color: rgba(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="LC1688" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// otherwise false</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1689" style="width: 35px; color: rgba(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="LC1689" class="line" lang="cpp">          <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequenceCheck</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BARCODE</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1690" style="width: 35px; color: rgba(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="LC1690" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">not</span> <span class="n" style="color: #333;">seqOk</span><span class="p">){</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1691" style="width: 35px; color: rgba(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="LC1691" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If the barcode contained invalid nucleotides</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1692" style="width: 35px; color: rgba(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="LC1692" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// this attempts to replace the first one with an `A`.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1693" style="width: 35px; color: rgba(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="LC1693" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// If this returns true, there was only one `N` and we</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1694" style="width: 35px; color: rgba(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="LC1694" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// replaced it; otherwise there was more than one `N`</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1695" style="width: 35px; color: rgba(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="LC1695" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// and the barcode sequence should be treated as invalid.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1696" style="width: 35px; color: rgba(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="LC1696" class="line" lang="cpp">            <span class="n" style="color: #333;">seqOk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">recoverBarcode</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1697" style="width: 35px; color: rgba(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="LC1697" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1699" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1662" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1700" style="width: 35px; color: rgba(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="LC1700" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If we have a barcode sequence, but not yet an index</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1694" style="width: 35px; color: rgba(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="1732" style="width: 35px; color: rgba(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">@@ -1694,7 +1732,7 @@ void processReadsQuasi(</td>

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<pre style="margin: 0;"> <span id="LC1732" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">barcodeIdx</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">//corrBarcodeIndex = barcodeMap[barcodeIndex];</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1696" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1734" style="width: 35px; color: rgba(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="LC1734" class="line" lang="cpp">          <span class="n" style="color: #333;">jointHitGroup</span><span class="p">.</span><span class="n" style="color: #333;">setBarcode</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">barcodeIdx</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="1735" 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="LC1697" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">alevinOpts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">p</span>rotocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1698" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1735" style="width: 35px; color: rgba(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="LC1735" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aut</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extractUMI</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">rp</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">localP</span>rotocol</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1736" style="width: 35px; color: rgba(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="LC1736" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1737" style="width: 35px; color: rgba(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="LC1737" 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;">umi_ok</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1738" style="width: 35px; color: rgba(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="LC1738" class="line" lang="cpp">            <span class="n" style="color: #333;">smallSeqs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2700" style="width: 35px; color: rgba(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">@@ -2662,7 +2700,8 @@ void alevinOptimize( std::vector<std::string>& trueBarcodesVec,</td>

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<td class="new_line diff-line-num" data-linenumber="2700" style="width: 35px; color: rgba(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="LC2700" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">ProtocolT</span><span class="p">></span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2701" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ProtocolT</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2664" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="2702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2702" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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</td>

<td class="new_line diff-line-num old" data-linenumber="2703" 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="LC2665" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2703

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2703" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2704

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2704" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">){</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2666

</td>

<td class="new_line diff-line-num" data-linenumber="2705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2705

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<pre style="margin: 0;"> <span id="LC2705" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2667

</td>

<td class="new_line diff-line-num" data-linenumber="2706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2706

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2706" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2668

</td>

<td class="new_line diff-line-num" data-linenumber="2707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2707

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2707" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2689" style="width: 35px; color: rgba(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="2728" style="width: 35px; color: rgba(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">@@ -2689,13 +2728,12 @@ int alevin_sc_align(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2689

</td>

<td class="new_line diff-line-num" data-linenumber="2728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2728

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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2690

</td>

<td class="new_line diff-line-num" data-linenumber="2729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2729

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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// ==== END: Library format processing ===</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2691

</td>

<td class="new_line diff-line-num" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2730

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2730" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2692" 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">

2692

</td>

<td class="new_line diff-line-num old" data-linenumber="2731" 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="LC2692" class="line" lang="cpp">    <span class="n" style="color: #333;">SalmonIndexVersionInfo</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2693" 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">

2693

</td>

<td class="new_line diff-line-num old" data-linenumber="2731" 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="LC2693" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">versionPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"versionInfo.json"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2694" 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">

2694

</td>

<td class="new_line diff-line-num old" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2694" class="line" lang="cpp">    <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">versionPath</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2695

</td>

<td class="new_line diff-line-num old" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2695" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">idxType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2731

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2731" 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;">salmonIndex</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2732

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2732" class="line" lang="cpp">      <span class="n" style="color: #333;">salmonIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">checkLoadIndex</span><span class="p">(</span><span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2733

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2733" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">idxType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">salmonIndex</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2696

</td>

<td class="new_line diff-line-num" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2734

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2734" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2697

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<td class="new_line diff-line-num" data-linenumber="2735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2735

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<pre style="margin: 0;"> <span id="LC2735" class="line" lang="cpp">    <span class="n" style="color: #333;">MappingStatistics</span> <span class="n" style="color: #333;">mstats</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2698" 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">

2698

</td>

<td class="new_line diff-line-num old" data-linenumber="2736" 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="LC2698" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">indexDirectory</span></span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2736

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<pre style="margin: 0;">+<span id="LC2736" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">salmonIndex</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2699

</td>

<td class="new_line diff-line-num" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2737

</td>

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<pre style="margin: 0;"> <span id="LC2737" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2700

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<td class="new_line diff-line-num" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2738

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<pre style="margin: 0;"> <span id="LC2738" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We currently do not support decoy sequence in the </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2701

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<td class="new_line diff-line-num" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2739

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<pre style="margin: 0;"> <span id="LC2739" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// --justAlign or --sketch modes, so check that the </span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2778" style="width: 35px; color: rgba(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="2816" style="width: 35px; color: rgba(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">@@ -2778,7 +2816,8 @@ int alevinQuant(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2778

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<td class="new_line diff-line-num" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2816

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<pre style="margin: 0;"> <span id="LC2816" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2779

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<td class="new_line diff-line-num" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2817

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<pre style="margin: 0;"> <span id="LC2817" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2780

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<td class="new_line diff-line-num" data-linenumber="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2818

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<pre style="margin: 0;"> <span id="LC2818" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2781" 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">

2781

</td>

<td class="new_line diff-line-num old" data-linenumber="2819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2781" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2819

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<pre style="margin: 0;">+<span id="LC2819" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2820

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2820" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">){</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2782

</td>

<td class="new_line diff-line-num" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2821

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<pre style="margin: 0;"> <span id="LC2821" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2783

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<td class="new_line diff-line-num" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2822

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<pre style="margin: 0;"> <span id="LC2822" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2784

</td>

<td class="new_line diff-line-num" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2823

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<pre style="margin: 0;"> <span id="LC2823" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2804" style="width: 35px; color: rgba(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="2843" style="width: 35px; color: rgba(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">@@ -2804,14 +2843,12 @@ int alevinQuant(AlevinOpts<ProtocolT>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="2804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2804

</td>

<td class="new_line diff-line-num" data-linenumber="2843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2843

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2843" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2805

</td>

<td class="new_line diff-line-num" data-linenumber="2844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2844

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2844" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2806

</td>

<td class="new_line diff-line-num" data-linenumber="2845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2845

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2845" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// ==== END: Library format processing ===</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2807" 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">

2807

</td>

<td class="new_line diff-line-num old" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2807" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2808" 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">

2808

</td>

<td class="new_line diff-line-num old" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2808" class="line" lang="cpp">    <span class="n" style="color: #333;">SalmonIndexVersionInfo</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2809" 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">

2809

</td>

<td class="new_line diff-line-num old" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2809" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">versionPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"versionInfo.json"</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2810" 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">

2810

</td>

<td class="new_line diff-line-num old" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2810" class="line" lang="cpp">    <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">versionPath</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2811" 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">

2811

</td>

<td class="new_line diff-line-num old" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2811" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">idxType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2846

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2846" 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;">salmonIndex</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2847

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2847" class="line" lang="cpp">      <span class="n" style="color: #333;">salmonIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">checkLoadIndex</span><span class="p">(</span><span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2848

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2848" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">idxType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">salmonIndex</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2812

</td>

<td class="new_line diff-line-num" data-linenumber="2849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2849

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2849" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2813

</td>

<td class="new_line diff-line-num" data-linenumber="2850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2850

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2850" class="line" lang="cpp">    <span class="n" style="color: #333;">MappingStatistics</span> <span class="n" style="color: #333;">mstats</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="2814" 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">

2814

</td>

<td class="new_line diff-line-num old" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2814" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">indexDirectory</span></span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2851

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2851" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">salmonIndex</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2815

</td>

<td class="new_line diff-line-num" data-linenumber="2852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2852

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2852" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//experiment.computePolyAPositions();</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2816

</td>

<td class="new_line diff-line-num" data-linenumber="2853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2853

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2853" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2817

</td>

<td class="new_line diff-line-num" data-linenumber="2854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2854

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2854" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// This will be the class in charge of maintaining our</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2996" style="width: 35px; color: rgba(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="3033" style="width: 35px; color: rgba(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">@@ -2996,133 +3033,132 @@ int alevinQuant(AlevinOpts<ProtocolT>& aopt,</td>

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<pre style="margin: 0;"> <span id="LC3033" class="line" lang="cpp"></span>

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<td class="new_line diff-line-num" data-linenumber="3034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3034" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">apt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protocols</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC3035" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC2999" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC3000" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DropSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3001" 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="LC3001" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="3002" 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="LC3002" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3036" 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="LC3003" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="3004" style="width: 35px; color: rgba(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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3036

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<pre style="margin: 0;"> <span id="LC3036" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3005" 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">

3005

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<pre style="margin: 0;">-<span id="LC3005" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DropSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3037" 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="LC3006" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3037" 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="LC3007" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3008" 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="LC3008" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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3009

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<pre style="margin: 0;">-<span id="LC3009" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3010" 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">

3010

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<td class="new_line diff-line-num old" data-linenumber="3037" 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="LC3010" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3011" 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="LC3011" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3012" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3013" 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">

3013

</td>

<td class="new_line diff-line-num old" data-linenumber="3037" 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="LC3013" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3037

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3037" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DropSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3038

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<pre style="margin: 0;">+<span id="LC3038" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3039

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<pre style="margin: 0;">+<span id="LC3039" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3040

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3040" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3041

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3041" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3042

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3042" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DropSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3043

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3043" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3044

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<pre style="margin: 0;">+<span id="LC3044" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3045

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3045" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3046

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3046" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3047

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3047" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3048

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<pre style="margin: 0;">+<span id="LC3048" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3014

</td>

<td class="new_line diff-line-num" data-linenumber="3049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3049

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3049" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3015" 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">

3015

</td>

<td class="new_line diff-line-num old" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3015" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3016" 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">

3016

</td>

<td class="new_line diff-line-num old" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3016" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3017" 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">

3017

</td>

<td class="new_line diff-line-num old" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3017" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3018" 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">

3018

</td>

<td class="new_line diff-line-num old" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3018" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3019

</td>

<td class="new_line diff-line-num" data-linenumber="3050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3050" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3020" 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">

3020

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3020" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3021" 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">

3021

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3021" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3022" 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">

3022

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3022" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3023" 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">

3023

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3023" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3024" 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">

3024

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3024" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3025" 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">

3025

</td>

<td class="new_line diff-line-num old" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3025" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3051

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3051" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3052

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3052" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3053

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3053" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3054

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3054" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3055

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3055" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CITESeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3056

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3056" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3057

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3057" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3058

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3058" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3059

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3059" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3060

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3060" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3061

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3061" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3062

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3062" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3063

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3063" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3064

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3064" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDropV2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3026

</td>

<td class="new_line diff-line-num" data-linenumber="3065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3065

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3065" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3027" 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">

3027

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3027" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3028" 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">

3028

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3028" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3029" 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">

3029

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3029" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3030" 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">

3030

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3030" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3031" 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">

3031

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3031" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3032" 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">

3032

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3032" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3033" 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">

3033

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3033" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3034" 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">

3034

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3034" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3035" 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">

3035

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3035" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3036" 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">

3036

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3036" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3037" 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">

3037

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3037" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3038" 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">

3038

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3038" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3039" 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">

3039

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3039" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3040" 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">

3040

</td>

<td class="new_line diff-line-num old" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3040" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3066

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3066" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3067

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3067" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3068

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3068" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDropV2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3069

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3069" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3070

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3070" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3071

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3071" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3072

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3072" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3073

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3073" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3074

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3074" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3075

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3075" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3076

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3076" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3077

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3077" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChromiumV3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3041

</td>

<td class="new_line diff-line-num" data-linenumber="3078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3078

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3078" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3042" 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">

3042

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3042" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3043" 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">

3043

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3043" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3044" 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">

3044

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3044" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3045" 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">

3045

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3045" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3046" 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">

3046

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3046" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChromiumV3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3047" 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">

3047

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3047" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3048" 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">

3048

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3048" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3049" 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">

3049

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3049" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3050" 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">

3050

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3050" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChromiumV3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3051" 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">

3051

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3051" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3052" 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">

3052

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3052" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3053" 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">

3053

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3053" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3054" 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">

3054

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3054" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3055" 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">

3055

</td>

<td class="new_line diff-line-num old" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3055" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3079

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3079" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3080

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3080" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3081

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3081" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ChromiumV3</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3082

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3082" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3083

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3083" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3084

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3084" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3085

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3085" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3086

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3086" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3087

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3087" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3088

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3088" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3089

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3089" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3090

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3090" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3056

</td>

<td class="new_line diff-line-num" data-linenumber="3091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3091

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3091" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3057" 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">

3057

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3057" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3058" 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">

3058

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3058" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3059" 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">

3059

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3059" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3060" 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">

3060

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3060" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3061" 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">

3061

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3061" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3062" 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">

3062

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3062" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3063" 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">

3063

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3063" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3064" 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">

3064

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3064" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3065" 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">

3065

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3065" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3066" 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">

3066

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3066" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3067" 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">

3067

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3067" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3068" 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">

3068

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3068" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3069" 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">

3069

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3069" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3070" 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">

3070

</td>

<td class="new_line diff-line-num old" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3070" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3092

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3092" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3093

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3093" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3094

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3094" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Chromium</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3095

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3095" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3096

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3096" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3097

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3097" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3098

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3098" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3099

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3099" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3100

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3100" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3101

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3101" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3102

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3102" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3103

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3103" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gemcode</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3071

</td>

<td class="new_line diff-line-num" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3104

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3104" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3072" 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">

3072

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3072" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3073" 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">

3073

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3073" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3074" 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">

3074

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3074" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3075" 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">

3075

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3075" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3076" 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">

3076

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3076" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gemcode</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3077" 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">

3077

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3077" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3078" 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">

3078

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3078" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3079" 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">

3079

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3079" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3080" 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">

3080

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3080" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gemcode</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3081" 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">

3081

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3081" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3082" 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">

3082

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3082" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3083" 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">

3083

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3083" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3084" 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">

3084

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3084" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3085" 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">

3085

</td>

<td class="new_line diff-line-num old" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3085" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3105

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3105" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3106

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3106" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3107

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3107" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Gemcode</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3108

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3108" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3109

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3109" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3110

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3110" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3111

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3111" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3112

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3112" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3113

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3113" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3114

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3114" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3115

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3115" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3116

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3116" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3086

</td>

<td class="new_line diff-line-num" data-linenumber="3117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3117

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3117" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3087" 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">

3087

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3087" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3088" 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">

3088

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3088" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3089" 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">

3089

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3089" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3090" 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">

3090

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3090" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3091" 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">

3091

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3091" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3092" 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">

3092

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3092" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3093" 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">

3093

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3093" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3094" 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">

3094

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3094" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3095" 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">

3095

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3095" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3096" 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">

3096

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3096" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3097" 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">

3097

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3097" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3098" 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">

3098

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3098" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3099" 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">

3099

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3099" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3100" 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">

3100

</td>

<td class="new_line diff-line-num old" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3100" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3118

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3118" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3119

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3119" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3120

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3120" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3121

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3121" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3122

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3122" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3123

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3123" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3124

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3124" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3125

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3125" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3126

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3126" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3127

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3127" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3128

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3128" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3129

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3129" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3101

</td>

<td class="new_line diff-line-num" data-linenumber="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3130

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3130" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3102" 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">

3102

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3102" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3103" 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">

3103

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3103" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3104" 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">

3104

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3104" class="line" lang="cpp">                </span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="3105" 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">

3105

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3105" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3106" 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">

3106

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3106" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3107" 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">

3107

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3107" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3108" 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">

3108

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3108" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3109" 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">

3109

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3109" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3110" 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">

3110

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3110" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3111" 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">

3111

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3111" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3112" 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">

3112

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3112" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3113" 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">

3113

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3113" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3114" 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">

3114

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3114" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3115" 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">

3115

</td>

<td class="new_line diff-line-num old" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3115" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3131

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3131" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3132

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3132" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3133

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3133" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CELSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3134

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3134" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3135

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3135" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3136

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3136" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3137

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3137" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3138

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3138" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3139

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3139" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3140

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3140" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3141

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3141" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3142

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3142" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3116

</td>

<td class="new_line diff-line-num" data-linenumber="3143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3143

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3143" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3117" 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">

3117

</td>

<td class="new_line diff-line-num old" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3117" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3118" 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">

3118

</td>

<td class="new_line diff-line-num old" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3118" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3144

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3144" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3145

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3145" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3146

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3146" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3147

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3147" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">QuartzSeq2</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3148

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3148" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3149

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3149" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3150

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3150" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3151

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3151" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3152

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3152" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3153

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3153" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3119

</td>

<td class="new_line diff-line-num" data-linenumber="3154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3154

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3154" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3120

</td>

<td class="new_line diff-line-num" data-linenumber="3155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3155

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3155" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3121" 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">

3121

</td>

<td class="new_line diff-line-num old" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3121" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">Quartz</span>Seq<span class="idiff right">2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3156

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<pre style="margin: 0;">+<span id="LC3156" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">Sci</span>Seq<span class="idiff right">3</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3122

</td>

<td class="new_line diff-line-num" data-linenumber="3157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3157

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<pre style="margin: 0;"> <span id="LC3157" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3123" 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">

3123

</td>

<td class="new_line diff-line-num old" data-linenumber="3158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3123" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3158

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3158" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3159

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3159" class="line" lang="cpp">                    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3124

</td>

<td class="new_line diff-line-num" data-linenumber="3160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3160

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3160" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3125" 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">

3125

</td>

<td class="new_line diff-line-num old" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3125" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">Quartz</span>Seq<span class="idiff right">2</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3161

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3161" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left">Sci</span>Seq<span class="idiff right">3</span></span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3126

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<td class="new_line diff-line-num" data-linenumber="3162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3162

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<pre style="margin: 0;"> <span id="LC3162" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="3127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3127

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<td class="new_line diff-line-num" data-linenumber="3163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3163

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3163" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3128

</td>

<td class="new_line diff-line-num" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3164

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3164" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3166" style="width: 35px; color: rgba(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">@@ -3130,34 +3166,34 @@ int alevinQuant(AlevinOpts<apt::QuartzSeq2>& aopt,</td>

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<td class="old_line diff-line-num" data-linenumber="3130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3130

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<td class="new_line diff-line-num" data-linenumber="3166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3166

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<pre style="margin: 0;"> <span id="LC3166" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3131

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<td class="new_line diff-line-num" data-linenumber="3167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3167

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<pre style="margin: 0;"> <span id="LC3167" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3132

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<td class="new_line diff-line-num" data-linenumber="3168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3168

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<pre style="margin: 0;"> <span id="LC3168" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3133" 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">

3133

</td>

<td class="new_line diff-line-num old" data-linenumber="3169" 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="LC3133" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3169

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3169" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3170

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<pre style="margin: 0;">+<span id="LC3170" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3134

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<td class="new_line diff-line-num" data-linenumber="3171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3171

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<pre style="margin: 0;"> <span id="LC3171" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3135" 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">

3135

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<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3135" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3136" 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">

3136

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" 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="LC3136" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3137" 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">

3137

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3137" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3138" 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">

3138

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3138" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3139" 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">

3139

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3139" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3140" 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">

3140

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3140" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CustomGeometry</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3141" 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">

3141

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3141" class="line" lang="cpp">                    <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3142" 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">

3142

</td>

<td class="new_line diff-line-num old" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3142" class="line" lang="cpp">                    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3143

</td>

<td class="new_line diff-line-num" data-linenumber="3172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3172

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3172" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3144" 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">

3144

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3144" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3145" 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">

3145

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3145" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3146" 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">

3146

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3146" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3147" 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">

3147

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3147" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3148" 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">

3148

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3148" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3149" 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">

3149

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3149" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3150" 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">

3150

</td>

<td class="new_line diff-line-num old" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3150" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3173

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3173" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3174

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3174" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3151

</td>

<td class="new_line diff-line-num" data-linenumber="3175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3175

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3175" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3152" 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">

3152

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3152" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3153" 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">

3153

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3153" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3154" 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">

3154

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3154" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3155" 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">

3155

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3155" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CustomGeometry</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3156" 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">

3156

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3156" class="line" lang="cpp">                <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3157" 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">

3157

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3157" class="line" lang="cpp">                <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3158" 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">

3158

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3158" class="line" lang="cpp">                <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3159" 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">

3159

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3159" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="3160" 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">

3160

</td>

<td class="new_line diff-line-num old" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3160" class="line" lang="cpp">                <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3176

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3176" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3177

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3177" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3178

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3178" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3179

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3179" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3180

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3180" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3181

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3181" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3182

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3182" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3183

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3183" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3184

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3184" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3185

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3185" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3186

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3186" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3187

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3187" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3188

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<pre style="margin: 0;">+<span id="LC3188" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevin_sc_align</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CustomGeometry</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3161

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<td class="new_line diff-line-num" data-linenumber="3189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3189

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<pre style="margin: 0;"> <span id="LC3189" class="line" lang="cpp">                <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3162" 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">

3162

</td>

<td class="new_line diff-line-num old" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3162" class="line" lang="cpp">                <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="3163" 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">

3163

</td>

<td class="new_line diff-line-num old" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3163" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span></pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3190

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3190" class="line" lang="cpp">                <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3191

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<pre style="margin: 0;">+<span id="LC3191" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3192

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3192" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3193

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3193" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">alevinQuant</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">apt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CustomGeometry</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span> <span class="n" style="color: #333;">SalmonOpts</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3194

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3194" class="line" lang="cpp">            <span class="n" style="color: #333;">SoftMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">barcodeMap</span><span class="p">,</span> <span class="n" style="color: #333;">TrueBcsT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3195

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3195" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">txpToGeneMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3196

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3196" class="line" lang="cpp">            <span class="n" style="color: #333;">spp</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sparse_hash_map</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;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">geneIdxMap</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3197

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3197" class="line" lang="cpp">            <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parsed_options</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">orderedOptions</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3198

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3198" class="line" lang="cpp">            <span class="n" style="color: #333;">CFreqMapT</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">freqCounter</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3199

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3199" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SalmonIndex</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">salmonIndex</span><span class="p">);</span></span></pre>

</td>

</tr>

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<br>

</li>

<li id="048f27201dad07181046acde7ff740937d795521">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#048f27201dad07181046acde7ff740937d795521"><strong>src/SalmonQuantMerge.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">@@ -27,6 +27,7 @@</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// C++ string formatting library #include "spdlog/fmt/fmt.h"</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// logger includes</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "spdlog/spdlog.h"</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "SalmonIndex.hpp"</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TargetColumn</span> <span class="p">{</span> <span class="n" style="color: #333;">LEN</span><span class="p">,</span> <span class="n" style="color: #333;">ELEN</span><span class="p">,</span> <span class="n" style="color: #333;">TPM</span><span class="p">,</span> <span class="n" style="color: #333;">NREADS</span> <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"></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">@@ -213,7 +214,7 @@ bool doMerge(QuantMergeOptions& qmOpts) {</td>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantMerge</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantMerge</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* salmonIndex */</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

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<br>

</li>

<li id="50bd7b80772108780ea31715fa1e48fc1610d64e">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#50bd7b80772108780ea31715fa1e48fc1610d64e"><strong>src/SalmonQuantify.cpp</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <functional></span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iterator></span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <map></span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <mutex></span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2385" style="width: 35px; color: rgba(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="2386" style="width: 35px; color: rgba(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">@@ -2385,7 +2386,7 @@ void quantifyLibrary(ReadExperimentT& experiment,</td>

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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="cpp">  <span class="n" style="color: #333;">jointLog</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"finished quantifyLibrary()"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC2388" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC2389" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">salmonIndex</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC2390" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="2392" style="width: 35px; color: rgba(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="LC2392" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2489" style="width: 35px; color: rgba(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="2490" style="width: 35px; color: rgba(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">@@ -2489,13 +2490,12 @@ transcript abundance from RNA-seq reads</td>

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<pre style="margin: 0;"> <span id="LC2490" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC2491" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// ==== END: Library format processing ===</span></span>

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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC2492" class="line" lang="cpp">    <span class="n" style="color: #333;">SalmonIndexVersionInfo</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="2493" 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="LC2493" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">versionPath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexDirectory</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"versionInfo.json"</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="2493" 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="LC2494" class="line" lang="cpp">    <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">versionPath</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2495" 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">

2495

</td>

<td class="new_line diff-line-num old" data-linenumber="2493" 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="LC2495" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">idxType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versionInfo</span><span class="p">.</span><span class="n" style="color: #333;">indexType</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2496" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2493" style="width: 35px; color: rgba(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="LC2493" 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;">salmonIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2496" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2494" style="width: 35px; color: rgba(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="LC2494" class="line" lang="cpp">      <span class="n" style="color: #333;">salmonIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">checkLoadIndex</span><span class="p">(</span><span class="n" style="color: #333;">indexDirectory</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">jointLog</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2496" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2495" style="width: 35px; color: rgba(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="LC2495" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="2496" style="width: 35px; color: rgba(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="LC2496" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="cpp">    <span class="n" style="color: #333;">MappingStatistics</span> <span class="n" style="color: #333;">mstats</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="2498" 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="LC2498" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">indexDirectory</span></span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2499" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2498" style="width: 35px; color: rgba(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="LC2498" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadExperimentT</span> <span class="n" style="color: #333;">experiment</span><span class="p">(</span><span class="n" style="color: #333;">readLibraries</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">salmonIndex</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">sopt</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2499" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="2499" style="width: 35px; color: rgba(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="LC2499" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2500" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="2500" style="width: 35px; color: rgba(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="LC2500" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// This will be the class in charge of maintaining our</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2501" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="2501" style="width: 35px; color: rgba(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="LC2501" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// rich equivalence classes</span></span>

</pre>

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<br>

</li>

<li id="271fbfae8ef9baaaaa6c951017faa5e410641190">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#271fbfae8ef9baaaaa6c951017faa5e410641190"><strong>src/SalmonQuantifyAlignments.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1573" style="width: 35px; color: rgba(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="1573" style="width: 35px; color: rgba(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">@@ -1573,7 +1573,7 @@ bool runSingleEndSample(std::vector<bfs::path>& alignmentFiles, bfs::path& trans</td>

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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">processSample</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">UnpairedRead</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">alnLib</span><span class="p">,</span> <span class="n" style="color: #333;">requiredObservations</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">,</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">outputDirectory</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1574" style="width: 35px; color: rgba(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="LC1574" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1575" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1575

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<pre style="margin: 0;"> <span id="LC1575" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1576" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1576" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">salmonAlignmentQuantify</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">SalmonIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* salmon_index */</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC1577" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">;</span></span>

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<br>

</li>

<li id="4da84e41d07b7f0b42dd57e484cdc5f4c6f8a496">

<a href="https://salsa.debian.org/med-team/salmon/-/commit/fdb785fce0b7e71707c500ef6243309fc9aa0edf#4da84e41d07b7f0b42dd57e484cdc5f4c6f8a496"><strong>src/WhiteList.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="260" style="width: 35px; color: rgba(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="260" style="width: 35px; color: rgba(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">@@ -260,7 +260,7 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useRibo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useMito</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="263" 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="LC263" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">performWhitelisting</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protocols</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">performWhitelisting</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protocols</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">InDrop<span class="idiff left right">V2</span></span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useRibo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useMito</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(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="288" style="width: 35px; color: rgba(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">@@ -288,6 +288,10 @@ namespace alevin {</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useRibo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useMito</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">performWhitelisting</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protocols</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SciSeq3</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useRibo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useMito</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numLowConfidentBarcode</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">performWhitelisting</span><span class="p">(</span><span class="n" style="color: #333;">AlevinOpts</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">alevin</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">protocols</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Custom</span><span class="p">></span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">aopt</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp">                                      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">trueBarcodes</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp">                                      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useRibo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useMito</span><span class="p">,</span></span>

</pre>

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