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<h3>
Alexandre Mestiashvili pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5">8fdd41ca</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2019-07-10T15:14:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.3+dfsg</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
</a>
</li>
<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#03d5fe68cb76a542cb9c06b8e03093e21319ca35">
blockwise_sa.h
</a>
</li>
<li class="file-stats">
<a href="#b8ddec6e882fec88e9f73fc947f13f9d54d7043e">
bowtie
</a>
</li>
<li class="file-stats">
<a href="#dfe5e559b6d490c25075d3912c6d2202202c6f72">
bowtie-inspect
</a>
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<li class="file-stats">
<a href="#ccc364c6c660e798a4f3c3b78119cbea257aee1e">
doc/manual.html
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<li class="file-stats">
<a href="#7d1f14ddcc3a740e3eeeaf356b4b0393ca8a50d2">
doc/website/latest-version.txt
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<li class="file-stats">
<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
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<li class="file-stats">
<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
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<li class="file-stats">
<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
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<li class="file-stats">
<a href="#9d7499ab4e42602402431f6e62fc3bab4336a91e">
ebwt.cpp
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<li class="file-stats">
<a href="#bdf1fda883543f04c4a046fdcaa8ba0db73fdb37">
ebwt.h
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<li class="file-stats">
<a href="#3b01777a95af313429e4b310e9c1f9f64244744b">
ebwt_build.cpp
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<li class="file-stats">
<a href="#325e44ac9e9631edc4f328e8eaa8247f8faaa318">
ebwt_search.cpp
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<li class="file-stats">
<a href="#78173a2355322cb62fac5714cd9aa8361ca724e7">
filebuf.h
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<li class="file-stats">
<a href="#f06297a2ada54367ed9d9c768f848c4726441af2">
hit.h
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<li class="file-stats">
<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
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<li class="file-stats">
<a href="#feeebf6c8e249c25303af46ea1abd54e5f54b5db">
processor_support.h
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<li class="file-stats">
<a href="#8cb73317275ca3f68e13f1344310abe501fa6653">
sam.cpp
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<li class="file-stats">
<a href="#cc60758ea89135534b00a4c0ae3e29ee95c0ef25">
<span class="new-file">
+
scripts/bowtie-hbb.sh
</span>
</a>
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<li class="file-stats">
<a href="#3dc9a13f2402854ca8fc5e4a0ced7b5d0012b83c">
<span class="new-file">
+
scripts/run-hbb.sh
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<li class="file-stats">
<a href="#1ba32b1a76b5b57a56e4d834114b45c9fbeb218e">
shmem.h
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</ul>
<h4>Changes:</h4>
<li id="f11fb3bba37e7060bedcd5895812b7c511c52651">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#f11fb3bba37e7060bedcd5895812b7c511c52651"><strong>MANUAL</strong></a>
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<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="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="199" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -199,7 +199,7 @@ Note that [Maq] internally rounds base qualities to the nearest 10 and</td>
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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(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="LC199" class="line" lang="plaintext">rounds qualities greater than 30 to 30. To maintain compatibility,</span>
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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
200
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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(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="LC200" class="line" lang="plaintext">Bowtie does the same. Rounding can be suppressed with the</span>
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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(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="LC201" class="line" lang="plaintext">`--nomaqround` option.</span>
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202
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<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(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="diff-line-num new_line" data-linenumber="203" style="width: 35px; color: rgba(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="LC203" class="line" lang="plaintext">Bowtie is not fully sensitive in `-n` 2 and `-n` 3 modes by default.</span>
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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
204
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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(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="LC204" class="line" lang="plaintext">In these modes Bowtie imposes a "backtracking limit" to limit effort</span>
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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">spent trying to find valid alignments for low-quality reads unlikely to</span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,7 +352,7 @@ output no alignments.</td>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="plaintext">Specifying `-m` 5 instructs bowtie to refrain from reporting any</span>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">alignments for reads having more than 5 reportable alignments. Since</span>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext">the read has exactly 5 reportable alignments, the `-m` 5 limit allows</span>
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<td class="diff-line-num old old_line" 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">
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="plaintext">`bowtie` to print them as usual.<span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">`bowtie` to print them as usual.</span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="plaintext"> Example 9: `-a -m 3 --best --strata`</span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); 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="383" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -383,7 +383,7 @@ A valid paired-end alignment satisfies these criteria:</td>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="plaintext"> defined by the `-v`/`-n`/`-e`/`-l` options.</span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="plaintext">2. The relative orientation and position of the mates satisfy the</span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="plaintext"> constraints defined by the `-I`/`-X`/`--fr`/`--rf`/`--ff`</span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="plaintext"> options.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"> options.</span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="plaintext"></span>
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388
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="plaintext">Policies governing which paired-end alignments are reported for a</span>
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389
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="plaintext">given read are specified using the `-k`, `-a` and `-m` options as</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">@@ -705,6 +705,18 @@ The query input files (specified either as `<m1>` and `<m2>`, or as</td>
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705
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="plaintext">or similar). All quality values are assumed to be 40 on the [Phred</span>
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706
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="plaintext">quality] scale.</span>
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext"> -F</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext">Reads are substrings (k-mers) extracted from a FASTA file `s`.</span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext">Specifically, for every reference sequence in FASTA file `s`, Bowtie</span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext">2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the</span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext">end of the reference. Each k-mer is aligned as a separate read.</span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext">Quality values are set to all Is (40 on Phred scale). Each k-mer</span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">(read) is given a name like `sequence`_`offset`, where `sequence`</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext">is the name of the FASTA sequence it was drawn from and `offset`</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext">is its 0-based offset of origin with respect to the sequence. Only</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext">single k-mers, i.e. unpaired reads, can be aligned in this way.</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext"></span>
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708
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="plaintext"> -r</span>
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709
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="plaintext"></span>
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710
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="plaintext">The query input files (specified either as `<m1>` and `<m2>`, or as</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">@@ -786,7 +798,7 @@ versions prior to 1.3. Default: off.</td>
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786
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="plaintext"> --solexa1.3-quals</span>
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787
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="plaintext"></span>
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788
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="plaintext">Same as `--phred64-quals`. This is usually the right option for use</span>
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789
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="plaintext">with (unconverted) reads emitted by GA Pipeline version 1.3 or later.<span class="idiff left right"> </span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext">with (unconverted) reads emitted by GA Pipeline version 1.3 or later.</span>
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790
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="plaintext">Default: off.</span>
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791
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="plaintext"></span>
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792
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="plaintext"> --integer-quals</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1025,7 +1037,7 @@ disallowed via the `-k` option) and they fall into more than one</td>
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1025
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="plaintext">alignment "stratum", report only those alignments that fall into the</span>
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1026
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="plaintext">best stratum. By default, Bowtie reports all reportable alignments</span>
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1027
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="plaintext">regardless of whether they fall into multiple strata. When</span>
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1028
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="plaintext">`--strata` is specified, `--best` must also be specified.<span class="idiff left right"> </span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="plaintext">`--strata` is specified, `--best` must also be specified.</span>
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1029
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="plaintext"></span>
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1030
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="plaintext"> Output</span>
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1031
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1271,7 +1283,7 @@ Default `bowtie` output</td>
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1271
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="plaintext"> character of the alignment occurs</span>
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1272
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="plaintext"></span>
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1273
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="plaintext">5. Read sequence (reverse-complemented if orientation is `-`).</span>
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1274
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<pre style="margin: 0;">-<span id="LC1274" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="plaintext"></span>
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1275
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1287
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="plaintext"> If the read was in colorspace, then the sequence shown in this</span>
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1276
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1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="plaintext"> column is the sequence of *decoded nucleotides*, not the original</span>
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1277
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="plaintext"> colors. See the [Colorspace alignment] section for details about</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1280,7 +1292,7 @@ Default `bowtie` output</td>
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1280
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1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="plaintext">6. ASCII-encoded read qualities (reversed if orientation is `-`). The</span>
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1281
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1293
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="plaintext"> encoded quality values are on the Phred scale and the encoding is</span>
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1282
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<td class="diff-line-num new_line" data-linenumber="1294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="plaintext"> ASCII-offset by 33 (ASCII char `!`).</span>
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1283
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<td class="diff-line-num new_line old" data-linenumber="1295" style="width: 35px; color: rgba(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="LC1283" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="plaintext"></span>
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1284
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<td class="diff-line-num new_line" data-linenumber="1296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1296
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="plaintext"> If the read was in colorspace, then the qualities shown in this</span>
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1285
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<td class="diff-line-num new_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="plaintext"> column are the *decoded qualities*, not the original qualities.</span>
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1286
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="plaintext"> See the [Colorspace alignment] section for details about decoding.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1290" style="width: 35px; color: rgba(0,0,0,0.3); 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="1302" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1290,7 +1302,7 @@ Default `bowtie` output</td>
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1290
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="plaintext"> this read, this column contains the value of the ceiling,</span>
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1291
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<td class="diff-line-num new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="plaintext"> indicating that at least that many valid alignments were found in</span>
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1292
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="plaintext"> addition to the one reported.</span>
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1293
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<pre style="margin: 0;">-<span id="LC1293" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="plaintext"></span>
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1294
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="plaintext"> Otherwise, this column contains the number of other instances where</span>
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1295
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="plaintext"> the same sequence aligned against the same reference characters as</span>
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1296
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="plaintext"> were aligned against in the reported alignment. This is *not* the</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1304,7 +1316,7 @@ Default `bowtie` output</td>
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1304
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="plaintext"> mismatches in the alignment, this field is empty. A single</span>
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1305
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<td class="diff-line-num new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="plaintext"> descriptor has the format offset:reference-base>read-base. The</span>
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1306
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<td class="diff-line-num new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="plaintext"> offset is expressed as a 0-based offset from the high-quality (5')</span>
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1307
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<td class="diff-line-num new_line old" data-linenumber="1319" style="width: 35px; color: rgba(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="LC1307" class="line" lang="plaintext"> end of the read.<span class="idiff left right"> </span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="plaintext"> end of the read.</span>
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1308
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1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="plaintext"></span>
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1309
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1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="plaintext">SAM `bowtie` output</span>
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1310
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1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="plaintext">-------------------</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1390,7 +1402,7 @@ right, the fields are:</td>
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1390
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1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="plaintext">11. ASCII-encoded read qualities (reverse-complemented if the read</span>
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1391
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1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="plaintext"> aligned to the reverse strand). The encoded quality values are on</span>
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1392
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1404
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="plaintext"> the [Phred quality] scale and the encoding is ASCII-offset by 33</span>
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1393
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="plaintext"> (ASCII char `!`), similarly to a [FASTQ] file.<span class="idiff left right"> </span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="plaintext"> (ASCII char `!`), similarly to a [FASTQ] file.</span>
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1394
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1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="plaintext"></span>
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1395
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="plaintext">12. Optional fields. Fields are tab-separated. For descriptions of</span>
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1396
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="plaintext"> all possible optional fields, see the SAM format specification.</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">@@ -1441,10 +1453,10 @@ The `bowtie-build` indexer</td>
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1441
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1453
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="plaintext">`bowtie-build` outputs a set of 6 files with suffixes `.1.ebwt`,</span>
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1442
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1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="plaintext">`.2.ebwt`, `.3.ebwt`, `.4.ebwt`, `.rev.1.ebwt`, and `.rev.2.ebwt`. (If</span>
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1443
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1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="plaintext">the total length of all the input sequences is greater than about 4</span>
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1444
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<pre style="margin: 0;">-<span id="LC1444" class="line" lang="plaintext">billion, then the index files will end in `ebwtl` instead of `ebwt`.)<span class="idiff left right"> </span></span>
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1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="plaintext">billion, then the index files will end in `ebwtl` instead of `ebwt`.)</span>
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1445
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1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="plaintext">These files together constitute the index: they are all that is needed</span>
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1446
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="plaintext">to align reads to that reference. The original sequence files are no</span>
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1447
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<pre style="margin: 0;">-<span id="LC1447" class="line" lang="plaintext">longer used by Bowtie once the index is built.<span class="idiff left right"> </span></span>
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1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="plaintext">longer used by Bowtie once the index is built.</span>
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1448
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1460
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="plaintext"></span>
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1449
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1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="plaintext">Use of Karkkainen's [blockwise algorithm] allows `bowtie-build` to</span>
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1450
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1462
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="plaintext">trade off between running time and memory usage. `bowtie-build` has</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">@@ -1580,7 +1592,7 @@ governs how many rows get marked: the indexer will mark every 2^`<int>`</td>
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1580
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<pre style="margin: 0;"> <span id="LC1592" class="line" lang="plaintext">rows. Marking more rows makes reference-position lookups faster, but</span>
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1593
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<pre style="margin: 0;"> <span id="LC1593" class="line" lang="plaintext">requires more memory to hold the annotations at runtime. The default</span>
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<pre style="margin: 0;"> <span id="LC1594" class="line" lang="plaintext">is 5 (every 32nd row is marked; for human genome, annotations occupy</span>
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1583
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<pre style="margin: 0;">-<span id="LC1583" class="line" lang="plaintext">about 340 megabytes).<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="plaintext">about 340 megabytes).</span>
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1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="plaintext"> -t/--ftabchars <int></span>
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#465370da702349b6dcb3f9f2026872cad6877efa"><strong>MANUAL.markdown</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">@@ -207,7 +207,7 @@ Note that [Maq] internally rounds base qualities to the nearest 10 and</td>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown">rounds qualities greater than 30 to 30. To maintain compatibility,</span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown">Bowtie does the same. Rounding can be suppressed with the</span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">`--nomaqround`</span><span class="p">]</span> option.</span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown">Bowtie is not fully sensitive in <span class="p">[</span><span class="nv" style="color: #008080;">`-n`</span><span class="p">]</span> 2 and <span class="p">[</span><span class="nv" style="color: #008080;">`-n`</span><span class="p">]</span> 3 modes by default.</span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="markdown">In these modes Bowtie imposes a "backtracking limit" to limit effort</span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="markdown">spent trying to find valid alignments for low-quality reads unlikely to</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -362,7 +362,7 @@ output no alignments.</td>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="markdown">Specifying <span class="p">[</span><span class="nv" style="color: #008080;">`-m`</span><span class="p">]</span> 5 instructs bowtie to refrain from reporting any</span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="markdown">alignments for reads having more than 5 reportable alignments. Since</span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="markdown">the read has exactly 5 reportable alignments, the <span class="p">[</span><span class="nv" style="color: #008080;">`-m`</span><span class="p">]</span> 5 limit allows</span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bowtie`</span> to print them as usual.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bowtie`</span> to print them as usual.</span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Example 9: `-a -m 3 --best --strata`</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="markdown"></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">@@ -393,7 +393,7 @@ A valid paired-end alignment satisfies these criteria:</td>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="markdown"> defined by the <span class="p">[</span><span class="nv" style="color: #008080;">`-v`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`-n`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`-e`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`-l`</span><span class="p">]</span> options.</span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="markdown"><span class="p">2.</span> The relative orientation and position of the mates satisfy the</span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="markdown"> constraints defined by the <span class="p">[</span><span class="nv" style="color: #008080;">`-I`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`-X`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`--fr`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`--rf`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: #008080;">`--ff`</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="markdown"> options.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown"> options.</span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="markdown">Policies governing which paired-end alignments are reported for a</span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="markdown">given read are specified using the <span class="p">[</span><span class="nv" style="color: #008080;">`-k`</span><span class="p">]</span>, <span class="p">[</span><span class="nv" style="color: #008080;">`-a`</span><span class="p">]</span> and <span class="p">[</span><span class="nv" style="color: #008080;">`-m`</span><span class="p">]</span> options as</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">@@ -767,6 +767,24 @@ The query input files (specified either as `<m1>` and `<m2>`, or as</td>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="markdown">or similar). All quality values are assumed to be 40 on the <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Phred</span>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="markdown">quality] scale.</span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"bowtie-options-F"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-F`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie-options-F</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -F</span></span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="markdown">Reads are substrings (k-mers) extracted from a FASTA file <span class="sb" style="color: #d14;">`s`</span>.</span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="markdown">Specifically, for every reference sequence in FASTA file <span class="sb" style="color: #d14;">`s`</span>, Bowtie</span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="markdown">2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the</span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="markdown">end of the reference. Each k-mer is aligned as a separate read.</span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="markdown">Quality values are set to all Is (40 on Phred scale). Each k-mer</span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="markdown">(read) is given a name like <span class="sb" style="color: #d14;">`sequence`</span>_<span class="sb" style="color: #d14;">`offset`</span>, where <span class="sb" style="color: #d14;">`sequence`</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="markdown">is the name of the FASTA sequence it was drawn from and <span class="sb" style="color: #d14;">`offset`</span></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="markdown">is its 0-based offset of origin with respect to the sequence. Only</span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="markdown">single k-mers, i.e. unpaired reads, can be aligned in this way.</span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="markdown"></span>
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770
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"bowtie-options-r"</span><span class="nt" style="color: #000080;">></span></span>
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771
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="markdown"></span>
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772
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-r`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie-options-r</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">@@ -938,7 +956,7 @@ versions prior to 1.3. Default: off.</td>
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938
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td><td></span></span>
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939
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="markdown"></span>
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940
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="markdown">Same as <span class="p">[</span><span class="nv" style="color: #008080;">`--phred64-quals`</span><span class="p">]</span>. This is usually the right option for use</span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="markdown">with (unconverted) reads emitted by GA Pipeline version 1.3 or later.<span class="idiff left right"> </span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="markdown">with (unconverted) reads emitted by GA Pipeline version 1.3 or later.</span>
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942
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="markdown">Default: off.</span>
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943
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="markdown"></span>
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"bowtie-options-integer-quals"</span><span class="nt" style="color: #000080;">></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">@@ -1333,7 +1351,7 @@ disallowed via the [`-k`] option) and they fall into more than one</td>
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="markdown">alignment "stratum", report only those alignments that fall into the</span>
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1334
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="markdown">best stratum. By default, Bowtie reports all reportable alignments</span>
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="markdown">regardless of whether they fall into multiple strata. When</span>
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1336
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<pre style="margin: 0;">-<span id="LC1336" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">`--strata`</span><span class="p">]</span> is specified, <span class="p">[</span><span class="nv" style="color: #008080;">`--best`</span><span class="p">]</span> must also be specified.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">`--strata`</span><span class="p">]</span> is specified, <span class="p">[</span><span class="nv" style="color: #008080;">`--best`</span><span class="p">]</span> must also be specified.</span>
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1337
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1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="markdown"></span>
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1338
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr></span></span>
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1339
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1357
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="markdown"><span class="nt" style="color: #000080;"></table></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1781,7 +1799,7 @@ Default `bowtie` output</td>
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1781
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1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="markdown"> character of the alignment occurs</span>
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1782
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1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="markdown"></span>
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1783
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<td class="diff-line-num new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="markdown"><span class="p">5.</span> Read sequence (reverse-complemented if orientation is <span class="sb" style="color: #d14;">`-`</span>).</span>
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1784
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<td class="diff-line-num new_line old" data-linenumber="1802" style="width: 35px; color: rgba(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="LC1784" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1802
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<pre style="margin: 0;">+<span id="LC1802" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1785
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<td class="diff-line-num new_line" data-linenumber="1803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="markdown"><span class="sb" style="color: #d14;"> If the read was in colorspace, then the sequence shown in this</span></span>
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<td class="diff-line-num old_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1786
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<td class="diff-line-num new_line" data-linenumber="1804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="markdown"><span class="sb" style="color: #d14;"> column is the sequence of *decoded nucleotides*, not the original</span></span>
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<td class="diff-line-num old_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1787
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<td class="diff-line-num new_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1805
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="markdown"><span class="sb" style="color: #d14;"> colors. See the [Colorspace alignment] section for details about</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); 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="1808" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1790,7 +1808,7 @@ Default `bowtie` output</td>
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1790
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1808
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<pre style="margin: 0;"> <span id="LC1808" class="line" lang="markdown"><span class="p">6.</span> ASCII-encoded read qualities (reversed if orientation is <span class="sb" style="color: #d14;">`-`</span>). The</span>
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1791
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1809
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<pre style="margin: 0;"> <span id="LC1809" class="line" lang="markdown"> encoded quality values are on the Phred scale and the encoding is</span>
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1792
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1810
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<pre style="margin: 0;"> <span id="LC1810" class="line" lang="markdown"> ASCII-offset by 33 (ASCII char <span class="sb" style="color: #d14;">`!`</span>).</span>
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1793
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<pre style="margin: 0;">-<span id="LC1793" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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1811
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<pre style="margin: 0;">+<span id="LC1811" class="line" lang="markdown"></span>
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1794
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<td class="diff-line-num new_line" data-linenumber="1812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1812
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<pre style="margin: 0;"> <span id="LC1812" class="line" lang="markdown"><span class="sb" style="color: #d14;"> If the read was in colorspace, then the qualities shown in this</span></span>
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<td class="diff-line-num old_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1795
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<td class="diff-line-num new_line" data-linenumber="1813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1813
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<pre style="margin: 0;"> <span id="LC1813" class="line" lang="markdown"><span class="sb" style="color: #d14;"> column are the *decoded qualities*, not the original qualities.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1796
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<td class="diff-line-num new_line" data-linenumber="1814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1814
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<pre style="margin: 0;"> <span id="LC1814" class="line" lang="markdown"><span class="sb" style="color: #d14;"> See the [Colorspace alignment] section for details about decoding.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1818" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1800,7 +1818,7 @@ Default `bowtie` output</td>
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1800
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1818
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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="markdown"> this read, this column contains the value of the ceiling,</span>
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<td class="diff-line-num old_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1801
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<td class="diff-line-num new_line" data-linenumber="1819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1819
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<pre style="margin: 0;"> <span id="LC1819" class="line" lang="markdown"> indicating that at least that many valid alignments were found in</span>
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<td class="diff-line-num old_line" data-linenumber="1802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1802
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<td class="diff-line-num new_line" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1820
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<pre style="margin: 0;"> <span id="LC1820" class="line" lang="markdown"> addition to the one reported.</span>
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1803
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<pre style="margin: 0;">-<span id="LC1803" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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1821
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<pre style="margin: 0;">+<span id="LC1821" class="line" lang="markdown"></span>
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1804
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1822
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<pre style="margin: 0;"> <span id="LC1822" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Otherwise, this column contains the number of other instances where</span></span>
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1805
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1823
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<pre style="margin: 0;"> <span id="LC1823" class="line" lang="markdown"><span class="sb" style="color: #d14;"> the same sequence aligned against the same reference characters as</span></span>
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1806
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1824
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<pre style="margin: 0;"> <span id="LC1824" class="line" lang="markdown"><span class="sb" style="color: #d14;"> were aligned against in the reported alignment. This is *not* the</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1832" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1814,7 +1832,7 @@ Default `bowtie` output</td>
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1814
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1832
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<pre style="margin: 0;"> <span id="LC1832" class="line" lang="markdown"> mismatches in the alignment, this field is empty. A single</span>
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1815
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1833
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<pre style="margin: 0;"> <span id="LC1833" class="line" lang="markdown"> descriptor has the format offset:reference-base>read-base. The</span>
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1816
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1834
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<pre style="margin: 0;"> <span id="LC1834" class="line" lang="markdown"> offset is expressed as a 0-based offset from the high-quality (5')</span>
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1817
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<pre style="margin: 0;">-<span id="LC1817" class="line" lang="markdown"> end of the read.<span class="idiff left right"> </span></span>
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1835
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<pre style="margin: 0;">+<span id="LC1835" class="line" lang="markdown"> end of the read.</span>
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1818
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1836
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<pre style="margin: 0;"> <span id="LC1836" class="line" lang="markdown"></span>
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1819
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1837
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<pre style="margin: 0;"> <span id="LC1837" class="line" lang="markdown"><span class="gh" style="color: #999;">SAM `bowtie` output</span></span>
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1820
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1838
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<pre style="margin: 0;"> <span id="LC1838" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1934" style="width: 35px; color: rgba(0,0,0,0.3); 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="1952" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1934,7 +1952,7 @@ right, the fields are:</td>
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1934
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1952
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<pre style="margin: 0;"> <span id="LC1952" class="line" lang="markdown"><span class="p">11.</span> ASCII-encoded read qualities (reverse-complemented if the read</span>
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1935
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1953
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<pre style="margin: 0;"> <span id="LC1953" class="line" lang="markdown"> aligned to the reverse strand). The encoded quality values are on</span>
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1936
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1954
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<pre style="margin: 0;"> <span id="LC1954" class="line" lang="markdown"> the <span class="p">[</span><span class="nv" style="color: #008080;">Phred quality</span><span class="p">]</span> scale and the encoding is ASCII-offset by 33</span>
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1937
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<pre style="margin: 0;">-<span id="LC1937" class="line" lang="markdown"> (ASCII char <span class="sb" style="color: #d14;">`!`</span>), similarly to a <span class="p">[</span><span class="nv" style="color: #008080;">FASTQ</span><span class="p">]</span> file.<span class="idiff left right"> </span></span>
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1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="markdown"> (ASCII char <span class="sb" style="color: #d14;">`!`</span>), similarly to a <span class="p">[</span><span class="nv" style="color: #008080;">FASTQ</span><span class="p">]</span> file.</span>
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1938
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1956
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<pre style="margin: 0;"> <span id="LC1956" class="line" lang="markdown"></span>
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1939
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="markdown"><span class="p">12.</span> Optional fields. Fields are tab-separated. For descriptions of</span>
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1940
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1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="markdown"> all possible optional fields, see the SAM format specification.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); 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="2029" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2011,10 +2029,10 @@ The `bowtie-build` indexer</td>
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2011
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2029
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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bowtie-build`</span> outputs a set of 6 files with suffixes <span class="sb" style="color: #d14;">`.1.ebwt`</span>,</span>
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2012
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2030
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<pre style="margin: 0;"> <span id="LC2030" class="line" lang="markdown"><span class="sb" style="color: #d14;">`.2.ebwt`</span>, <span class="sb" style="color: #d14;">`.3.ebwt`</span>, <span class="sb" style="color: #d14;">`.4.ebwt`</span>, <span class="sb" style="color: #d14;">`.rev.1.ebwt`</span>, and <span class="sb" style="color: #d14;">`.rev.2.ebwt`</span>. (If</span>
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2013
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<td class="diff-line-num new_line" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="markdown">the total length of all the input sequences is greater than about 4</span>
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2014
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<td class="diff-line-num new_line old" data-linenumber="2032" style="width: 35px; color: rgba(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="LC2014" class="line" lang="markdown">billion, then the index files will end in <span class="sb" style="color: #d14;">`ebwtl`</span> instead of <span class="sb" style="color: #d14;">`ebwt`</span>.)<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="2015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2032
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<pre style="margin: 0;">+<span id="LC2032" class="line" lang="markdown">billion, then the index files will end in <span class="sb" style="color: #d14;">`ebwtl`</span> instead of <span class="sb" style="color: #d14;">`ebwt`</span>.)</span>
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2015
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<td class="diff-line-num new_line" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="markdown">These files together constitute the index: they are all that is needed</span>
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<td class="diff-line-num old_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2016
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<td class="diff-line-num new_line" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="markdown">to align reads to that reference. The original sequence files are no</span>
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<td class="diff-line-num old old_line" data-linenumber="2017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2017
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<td class="diff-line-num new_line old" data-linenumber="2035" style="width: 35px; color: rgba(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="LC2017" class="line" lang="markdown">longer used by Bowtie once the index is built.<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="2018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="markdown">longer used by Bowtie once the index is built.</span>
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<td class="diff-line-num old_line" data-linenumber="2018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2018
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<td class="diff-line-num new_line" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="2019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2019
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<td class="diff-line-num new_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="markdown">Use of Karkkainen's <span class="p">[</span><span class="nv" style="color: #008080;">blockwise algorithm</span><span class="p">]</span> allows <span class="sb" style="color: #d14;">`bowtie-build`</span> to</span>
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2020
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<td class="diff-line-num new_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2038
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<pre style="margin: 0;"> <span id="LC2038" class="line" lang="markdown">trade off between running time and memory usage. <span class="sb" style="color: #d14;">`bowtie-build`</span> has</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); 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="2239" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2221,7 +2239,7 @@ governs how many rows get marked: the indexer will mark every 2^`<int>`</td>
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<td class="diff-line-num old_line" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2221
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<td class="diff-line-num new_line" data-linenumber="2239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2239
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<pre style="margin: 0;"> <span id="LC2239" class="line" lang="markdown">rows. Marking more rows makes reference-position lookups faster, but</span>
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2222
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<td class="diff-line-num new_line" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="markdown">requires more memory to hold the annotations at runtime. The default</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2223
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<td class="diff-line-num new_line" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="markdown">is 5 (every 32nd row is marked; for human genome, annotations occupy</span>
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<td class="diff-line-num old old_line" data-linenumber="2224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2224
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<td class="diff-line-num new_line old" data-linenumber="2242" style="width: 35px; color: rgba(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="LC2224" class="line" lang="markdown">about 340 megabytes).<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="2225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2242
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<pre style="margin: 0;">+<span id="LC2242" class="line" lang="markdown">about 340 megabytes).</span>
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<td class="diff-line-num old_line" data-linenumber="2225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2225
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<td class="diff-line-num new_line" data-linenumber="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2243
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2243" class="line" lang="markdown"></span>
</pre>
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2226
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<td class="diff-line-num new_line" data-linenumber="2244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2244
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<pre style="margin: 0;"> <span id="LC2244" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td></span></span>
</pre>
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2227
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<td class="diff-line-num new_line" data-linenumber="2245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2245
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<pre style="margin: 0;"> <span id="LC2245" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); 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="2443" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2425,4 +2443,3 @@ Print version information and quit.</td>
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2425
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2443
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<pre style="margin: 0;"> <span id="LC2443" class="line" lang="markdown">Print usage information and quit.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2426
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2444
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2444" class="line" lang="markdown"></span>
</pre>
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2427
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<td class="diff-line-num new_line" data-linenumber="2445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2445
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<pre style="margin: 0;"> <span id="LC2445" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr></table></span></span></pre>
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<td class="diff-line-num old old_line" data-linenumber="2428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2428
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<td class="diff-line-num new_line old" data-linenumber="2446" style="width: 35px; color: rgba(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="LC2428" class="line" lang="markdown"></span></pre>
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<br>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -420,9 +420,10 @@ doc: doc/manual.html MANUAL</td>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="make"><span class="nl">doc/manual.html</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">MANUAL.markdown</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<h1>Table of Contents</h1>"</span> <span class="o" style="font-weight: 600;">></span> .tmp.head</span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="make"> pandoc <span class="nt" style="color: #000080;">-<span class="idiff left">T</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"Bowtie Manual"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>B</span> .tmp.head <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="make"> pandoc <span class="nt" style="color: #000080;">-B</span> .tmp.head <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="make"> <span class="nt" style="color: #000080;">--css</span> style.css <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="make"> <span class="nt" style="color: #000080;">--from</span> markdown <span class="nt" style="color: #000080;">--to</span> HTML <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="make"> <span class="nt" style="color: #000080;">--metadata</span> title:<span class="s2" style="color: #d14;">"Bowtie Manual"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="make"> <span class="nt" style="color: #000080;">--table-of-contents</span> <span class="nv" style="color: #008080;">$^</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="make"><span class="nl">MANUAL</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">MANUAL.markdown</span></span>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</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">@@ -5,14 +5,15 @@ Bowtie NEWS</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Bowtie is now available for download. 0.9.0 is the first version to</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">be released under the OSI Artistic License (see `LICENSE') and freely</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">available to the public for download. The current version is 1.2.<span class="idiff left right">1.1</span>.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">available to the public for download. The current version is 1.2.<span class="idiff left right">3</span>.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Reporting Issues</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">================</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">Please report any issues using the Sourceforge bug tracker:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> https://sourceforge.net/tracker/?group_id=236897&atid=1101606</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * https://github.com/BenLangmead/bowtie/issues</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * https://sourceforge.net/tracker/?group_id=236897&atid=1101606</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Announcements</span>
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<pre style="margin: 0;"> <span id="LC19" 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">@@ -26,7 +27,20 @@ subscribe to our mailing list:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Version Release History</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">=======================</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Version 1.2.3 - Jul 5, 2019</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * Added support for reading and inspecting Bowtie 2 indexes.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> * Added support for building an index from a gzipped-compressed</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> FASTA.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> * Fixed issue preventing bowtie from reporting repeated alignments</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> when -M is specified.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * Fixed issue with -F mode omitting final base of each read.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> * Fixed clipping of first letter of first read in batches after first.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> * Fixed an issue preventing bowtie wrapper script from finding indexes.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">Version 1.2.2 - Dec 11, 2017</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1).</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> * Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> * Fixed major issue with incorrect alignment offsets being reported in --large-index mode</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> * Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1.2.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1.2.<span class="idiff left right">3</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,7 +74,11 @@ class BlockwiseSA {</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">_logger</span><span class="p">(</span><span class="n" style="color: #333;">__logger</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BlockwiseSA</span><span class="p">()</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BlockwiseSA</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if __cplusplus > 199711L</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">noexcept</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="LC80" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Get the next suffix; compute the next bucket if necessary.</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">@@ -200,7 +204,11 @@ class KarkkainenBlockwiseSA : public InorderBlockwiseSA<TStr> {</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <span class="p">{</span> <span class="n" style="color: #333;">_randomSrc</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">__seed</span><span class="p">);</span> <span class="n" style="color: #333;">reset</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if __cplusplus > 199711L</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">noexcept</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="LC210" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="p">{</span></span>
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204
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_dc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">_dc</span><span class="p">;</span> <span class="n" style="color: #333;">_dc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// difference cover sample</span></span>
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205
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_done</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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206
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">_done</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#b8ddec6e882fec88e9f73fc947f13f9d54d7043e"><strong>bowtie</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">@@ -69,6 +69,7 @@ def main():</td>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span> <span class="n" style="color: #333;">bin_s</span><span class="p">)</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">bowtie_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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73
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>
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74
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">large_index</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -85,14 +86,16 @@ def main():</td>
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85
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tot_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">small_index_max_size</span><span class="p">:</span></span>
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86
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span> <span class="n" style="color: #333;">bin_l</span><span class="p">)</span></span>
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87
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_l</span><span class="p">):</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_s</span><span class="p">)</span>\</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_l</span><span class="p">):</span></span>
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89
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span> <span class="n" style="color: #333;">bin_l</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">bowtie_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">args</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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91
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bowtie_args</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</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="s" style="color: #d14;">'-'</span><span class="p">:</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_l</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_s</span><span class="p">)</span>\</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idx_ext_l</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span> <span class="n" style="color: #333;">bin_l</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">:</span></span>
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<li id="dfe5e559b6d490c25075d3912c6d2202202c6f72">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#dfe5e559b6d490c25075d3912c6d2202202c6f72"><strong>bowtie-inspect</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">@@ -34,8 +34,8 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bowtie-inspect"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bowtie-inspect-s"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bowtie-inspect-l"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">idx_ext_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.1.ebwtl'</span><span class="p"><span class="idiff left">;</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">idx_ext_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.1.ebwt'</span><span class="p"><span class="idiff left">;</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">idx_ext_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.1.ebwtl'</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">idx_ext_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.1.ebwt'</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">curr_script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">inspect</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsourcefile</span><span class="p">(</span><span class="n" style="color: #333;">main</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">ex_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">curr_script</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">inspect_bin_s</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">@@ -43,12 +43,13 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="p">,</span><span class="n" style="color: #333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bld</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">build_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--verbose'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">options</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'--verbose'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--debug'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">options</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_spec</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'-debug'</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_l</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'-debug'</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'--large-index'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">options</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">inspect_bin_l</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">arguments</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="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,18 +59,13 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">large_idx_exists</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">small_idx_exists</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">logging</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;">"No small index but a large one is present. Inspecting the large index."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">inspect_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">inspect_bin_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">arguments</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;">inspect_bin_name</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic-0'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">'--wrapper'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">logging</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;">'Command: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">inspect_bin_spec</span><span class="p">,</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">arguments</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])))</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execv</span><span class="p">(</span><span class="n" style="color: #333;">inspect_bin_spec</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execv</span><span class="p">(</span><span class="n" style="color: #333;">inspect_bin_spec</span><span class="p">,</span> <span class="n" style="color: #333;">arguments</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">0.12.8</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">i.2.3</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><h2>1.2.3 - 07/05/2019</h2></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <li>Added support for reading and inspecting Bowtie 2 indexes. Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2.</li></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <li>Added support for building an index from a gzipped-compressed FASTA.</li></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <li>Fixed issue preventing bowtie from reporting repeated alignments when <tt><a href="manual.shtml#bowtie-options-M">-M</a></tt> is specified.</li></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <li>Fixed issue with <tt><a href="manual.shtml#bowtie-options-F">-F</a></tt> mode omitting final base of each read.</li></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <li>Fixed clipping of first letter of first read in batches after first.</li></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <li>Fixed an issue preventing bowtie wrapper script from finding indexes.</li></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><h2>1000-Genomes major-allele SNP references -- 4/26/2019</h2></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <li>For each base where the typical reference has the non-majority allele (according to the <a href="http://www.internationalgenome.org">1000 Genomes Project</a>, we substituted in the majority allele instead</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <li>Links for indexes added to sidebar, as are links for the edited FASTA files</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> <li>We made versions both for GRCh38 primary assembly and hg19 assembly</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> <li>See <a href="https://github.com/BenLangmead/bowtie-majref">how we created them</a></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> <li>Only SNPs (single-base substitutions) are considered for now; indels are future work</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> <li>Because only SNPs are considered, coordinates (e.g. gene annotations) are the same as for typical GRCh38 and hg19 assemblies. Most downstream tools are unaffected as long as major-allele-edited FASTAs are used wherever genome sequences are required.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"><h2>1.2.2 - 12/11/2017</h2></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"><p>Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (<tt>make NO_TBB=1</tt>).</p></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"><ul></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> <li>Fixed major issue causing corrupt SAM output when using many threads (<span class="idiff left right">-p/--threads</span>) on certain systems</li></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> <li>Fixed major issue with incorrect alignment offsets being reported in <span class="idiff left right">--large-index</span> mode</li></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> <li>Fixed major issue with reads files being skipped when multiple inputs were specified together with <span class="idiff left right">-p/--threads</span></li></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> <li>Fixed major issue causing corrupt SAM output when using many threads (<span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-p">-p/--threads</a></tt></span>) on certain systems</li></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> <li>Fixed major issue with incorrect alignment offsets being reported in <span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-large-index">--large-index</a></tt></span> mode</li></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> <li>Fixed major issue with reads files being skipped when multiple inputs were specified together with <span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-p">-p/--threads</a></tt></span></li></span>
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6
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> <li>The official LICENSE of Bowtie was changed to Artistic License 2.0. This fixes an issue with the previous LICENSE, which mistakenly combined elements of different open-source licenses.</li></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> <li>Fixed issue where bowtie would still run for a long time even when <span class="idiff left right">-u</span> was set to a small number.</li></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> <li>Fixed issue where bowtie would still run for a long time even when <span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-u">-u</a></tt></span> was set to a small number.</li></span>
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8
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> <li>Fixed spurious "Reads file contained a pattern with more than 1024 quality values" error for some colorspace inputs.</li></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <li>Fixed issue with <span class="idiff left right">--strata</span> sometimes failing to suppress alignments at lower strata.</li></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <li>Fixed issue with ends of paired-end reads sometimes appearing in non-adjacent lines of the SAM output with <span class="idiff left right">-p/--threads</span> >1</li></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> <li>Fixed issue with <span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-strata">--strata</a></tt></span> sometimes failing to suppress alignments at lower strata.</li></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> <li>Fixed issue with ends of paired-end reads sometimes appearing in non-adjacent lines of the SAM output with <span class="idiff left right"><tt><a href="manual.shtml#bowtie-options-p">-p/--threads</a></tt></span> >1</li></span>
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11
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> <li>Fixed issue whereby the read name of end #2 was not always truncated at the first whitespace character</li></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> <li>Code simplifications</li></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></ul></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">@@ -18,10 +18,10 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> </tr></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> <td></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.<span class="idiff left right">2">Bowtie 1.2.2</span></a></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.<span class="idiff left right">3">Bowtie 1.2.3</span></a></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> </td></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">12/11/17</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">07/05/19</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">@@ -105,37 +105,67 @@</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> <!-- GRCh38 major-allele --></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> <tr><td></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj_bt.zip"><i>H. sapiens</i>, NCBI GRCh38 <br/> with 1KGenomes major SNPs</a></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> </td><td align="right"></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> <tr><td colspan="2" style="font-size: x-small"> <a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/grch38_1kgmaj.fa.gz">FASTA</a></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> <!-- hg19 --></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> <tr><td></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.zip"><i>H. sapiens</i>, UCSC hg19</a></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"> </td><td align="right"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> <!--</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> <tr></span>
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115
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.1.zip">part 1</a> - 1.7 GB,</span>
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116
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19.ebwt.2.zip">part 2</a> - 1.0 GB</td></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"> </tr><tr></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> </tr></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> --></span>
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130
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118
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> <td> colorspace:</span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_c.ebwt.zip">full</a>, or</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_c.ebwt.zip">full</a></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> <!-- , or</span>
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120
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_c.ebwt.1.zip">part 1</a>,</span>
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121
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_c.ebwt.2.zip">part 2</a></td></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> --></span>
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122
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> </tr></table></span>
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123
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> </td></tr></span>
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124
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> <!-- hg19 major-allele --></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> <tr><td></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_1kgmaj_bt.zip"><i>H. sapiens</i>, UCSC hg19 <br/> with 1KGenomes major SNPs</a></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> </td><td align="right"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> <tr><td colspan="2" style="font-size: x-small"> <a href="https://github.com/BenLangmead/bowtie-majref">How we built this</a>, <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg19_1kgmaj.fa.gz">FASTA</a></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> </td></tr></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"></span>
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125
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> <!-- hg18 --></span>
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126
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> <tr><td></span>
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127
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18.ebwt.zip"><i>H. sapiens</i>, UCSC hg18</a></span>
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128
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> </td><td align="right"></span>
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129
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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130
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> </td></tr></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> <!--</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> <tr></span>
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132
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18.ebwt.1.zip">part 1</a> - 1.7 GB,</span>
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133
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18.ebwt.2.zip">part 2</a> - 1.0 GB</td></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> </tr><tr></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> </tr></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> --></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> <tr></span>
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135
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"> <td> colorspace:</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18_c.ebwt.zip">full</a>, or</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18_c.ebwt.zip">full</a></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> <!-- , or</span>
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137
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18_c.ebwt.1.zip">part 1</a>,</span>
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138
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/hg18_c.ebwt.2.zip">part 2</a></td></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> --></span>
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139
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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">@@ -145,14 +175,20 @@</td>
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175
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146
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> </td></tr></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> <!--</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> <tr></span>
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149
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm.ebwt.1.zip">part 1</a> - 1.7 GB,</span>
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150
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm.ebwt.2.zip">part 2</a> - 1.0 GB</td></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> </tr><tr></span>
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183
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> --></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> <tr></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"> <td> colorspace:</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm_c.ebwt.zip">full</a>, or</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm_c.ebwt.zip">full</a></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> <!-- , or</span>
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154
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm_c.ebwt.1.zip">part 1</a>,</span>
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155
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_37_asm_c.ebwt.2.zip">part 2</a></td></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="plaintext"> </tr></table></span>
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194
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<pre style="margin: 0;"> <span id="LC194" 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">@@ -162,14 +198,20 @@</td>
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162
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext"> </td><td align="right"></span>
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163
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext"> <b>2.7 GB</b></span>
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164
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext"> </td></tr></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> <!--</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> <tr></span>
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166
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm.ebwt.1.zip">part 1</a> - 1.7 GB,</span>
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167
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm.ebwt.2.zip">part 2</a> - 1.0 GB</td></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> </tr><tr></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> </tr></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> <tr></span>
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169
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"> <td> colorspace:</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm_c.ebwt.zip">full</a>, or</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm_c.ebwt.zip">full</a></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> <!-- , or</span>
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171
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm_c.ebwt.1.zip">part 1</a>,</span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/h_sapiens_asm_c.ebwt.2.zip">part 2</a></td></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"> </tr></table></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="plaintext"> </td></tr></span>
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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>
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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">@@ -179,14 +221,20 @@</td>
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179
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext"> </td><td align="right"></span>
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180
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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181
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext"> </td></tr></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> <!--</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> <tr></span>
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183
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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<td class="diff-line-num old_line" 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">
184
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> </tr><tr></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> </tr></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> --></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> <tr></span>
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186
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext"> <td> colorspace:</span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8_c.ebwt.zip">full</a>, or</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8_c.ebwt.zip">full</a></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> <!-- , or</span>
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188
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8_c.ebwt.1.zip">part 1</a>,</span>
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189
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm8_c.ebwt.2.zip">part 2</a></td></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> --></span>
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190
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="plaintext"> </tr></table></span>
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191
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,14 +244,20 @@</td>
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196
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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(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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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> <!--</span>
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249
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200
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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201
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> </tr><tr></span>
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252
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext"> <td> colorspace:</span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9_c.ebwt.zip">full</a>, or</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9_c.ebwt.zip">full</a></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> <!-- , or</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9_c.ebwt.1.zip">part 1</a>,</span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/mm9_c.ebwt.2.zip">part 2</a></td></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext"> </tr></table></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,14 +267,20 @@</td>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> <!--</span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext"> </tr><tr></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext"> <td> colorspace:</span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37_c.ebwt.zip">full</a>, or</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37_c.ebwt.zip">full</a></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> <!-- , or</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37_c.ebwt.1.zip">part 1</a>,</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/m_musculus_ncbi37_c.ebwt.2.zip">part 2</a></td></span>
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<pre style="margin: 0;">+<span id="LC283" 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">@@ -230,14 +290,20 @@</td>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> <tr></span>
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234
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext"> </tr><tr></span>
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298
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> <tr></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext"> <td> colorspace:</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4_c.ebwt.zip">full</a>, or</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4_c.ebwt.zip">full</a></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> <!-- , or</span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4_c.ebwt.1.zip">part 1</a>,</span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/rn4_c.ebwt.2.zip">part 2</a></td></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext"> </tr></table></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -247,14 +313,20 @@</td>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> <!--</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> <tr></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> --></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext"> <td> colorspace:</span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus_c.ebwt.zip">full</a>, or</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus_c.ebwt.zip">full</a></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> <!-- , or</span>
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256
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus_c.ebwt.1.zip">part 1</a>,</span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/b_taurus_c.ebwt.2.zip">part 2</a></td></span>
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329
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<pre style="margin: 0;">+<span id="LC329" 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">@@ -264,14 +336,20 @@</td>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="plaintext"> <b>2.4 GB</b></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="plaintext"> </td></tr></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> <!--</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> <tr></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext"> <td> or: <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2.ebwt.1.zip">part 1</a> - 1.5 GB,</span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2.ebwt.2.zip">part 2</a> - 900 MB</td></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"> </tr><tr></span>
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346
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271
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="plaintext"> <td> colorspace:</span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2_c.ebwt.zip">full</a>, or</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2_c.ebwt.zip">full</a></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> <!-- , or</span>
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273
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2_c.ebwt.1.zip">part 1</a>,</span>
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274
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/canFam2_c.ebwt.2.zip">part 2</a></td></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> --></span>
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275
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext"> </td></tr></span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); 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="357" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -279,7 +357,7 @@</td>
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279
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="plaintext"> <tr><td></span>
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280
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/galGal3.ebwt.zip"><i>G. gallus</i>, UCSC, galGal3</a></span>
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281
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext"> </td><td align="right"></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext"> <span class="idiff left right">1.1 GB</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> <span class="idiff left right"><b>1.1 GB</b></span></span>
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283
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="plaintext"> </td></tr></span>
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284
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="plaintext"> <td> colorspace:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); 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="369" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -291,7 +369,7 @@</td>
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291
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="plaintext"> <tr><td></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/d_melanogaster_fb5_22.ebwt.zip"><i>D. melanogaster</i>, Flybase, r5.22</a></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="plaintext"> </td><td align="right"></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext"> <span class="idiff left right">150 MB</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"> <span class="idiff left right"><b>150 MB</b></span></span>
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295
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="plaintext"> </td></tr></span>
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296
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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297
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="plaintext"> <td> colorspace:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); 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="381" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -303,7 +381,7 @@</td>
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303
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="plaintext"> <tr><td></span>
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304
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/a_thaliana.ebwt.zip"><i>A. thaliana</i>, TAIR, TAIR9</a></span>
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305
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="plaintext"> </td><td align="right"></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext"> <span class="idiff left right">120 MB</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> <span class="idiff left right"><b>120 MB</b></span></span>
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307
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="plaintext"> </td></tr></span>
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308
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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309
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387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC387" class="line" lang="plaintext"> <td> colorspace:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,7 +393,7 @@</td>
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315
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="plaintext"> <tr><td></span>
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316
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/c_elegans_ws200.ebwt.zip"><i>C. elegans</i>, Wormbase, WS200</a></span>
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317
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="plaintext"> </td><td align="right"></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="plaintext"> <span class="idiff left right">75 MB</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"> <span class="idiff left right"><b>75 MB</b></span></span>
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319
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"> </td></tr></span>
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320
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<td class="diff-line-num 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">
321
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399
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC399" class="line" lang="plaintext"> <td> colorspace:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -327,7 +405,7 @@</td>
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327
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"> <tr><td></span>
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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
328
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<td class="diff-line-num new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/s_cerevisiae.ebwt.zip"><i>S. cerevisiae</i>, CYGD</a></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext"> <span class="idiff left right">15 MB</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext"> <span class="idiff left right"><b>15 MB</b></span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="plaintext"> <td> colorspace:</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">@@ -339,7 +417,7 @@</td>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="plaintext"> <a href="ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/e_coli.ebwt.zip"><i>E. coli</i>, NCBI, st. 536</a></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext"> <span class="idiff left right">5 MB</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext"> <span class="idiff left right"><b>5 MB</b></span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext"> <tr><td colspan=2><table width="100%"><tr></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext"> <td> colorspace:</span>
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<li id="9d7499ab4e42602402431f6e62fc3bab4336a91e">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#9d7499ab4e42602402431f6e62fc3bab4336a91e"><strong>ebwt.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">@@ -10,16 +10,17 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.h></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef BOWTIE_64BIT_INDEX</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC18" 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;">gEbwt_ext</span><span class="p">(</span><span class="s" style="color: #d14;">"ebwtl"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC19" 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;">gBt2_ext</span><span class="p">(</span><span class="s" style="color: #d14;">"bt2l"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" 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;">gEbwt_ext</span><span class="p">(</span><span class="s" style="color: #d14;">"ebwt"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC23" 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;">gBt2_ext</span><span class="p">(</span><span class="s" style="color: #d14;">"bt2"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></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;">#endif // BOWTIE_64BIT_INDEX</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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">@@ -33,12 +34,15 @@ string gLastIOErrMsg;</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * "$BOWTIE_INDEXES/".</span></span>
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<pre style="margin: 0;"> <span id="LC35" 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="LC36" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="nf" style="color: #900; font-weight: 600;">adjustEbwtBase</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cmdline</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"><span class="idiff left right"> </span> <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="LC37" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="idiff left right"> </span> <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="LC39" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Trying "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">access</span><span class="p">((</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gBt2_ext</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">R_OK</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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gBt2_ext</span><span class="p">;</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="p">}</span></span>
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42
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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">((</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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43
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47
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<pre style="margin: 0;"> <span id="LC47" 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;">in</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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44
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" didn't work"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +64,10 @@ string adjustEbwtBase(const string& cmdline,</td>
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60
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"BOWTIE_INDEXES"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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61
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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">str</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;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"BOWTIE_INDEXES"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">;</span></span>
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62
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Trying "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">((</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1.ebwt"</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">access</span><span class="p">((</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gBt2_ext</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">R_OK</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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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gBt2_ext</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">((</span><span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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64
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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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<pre style="margin: 0;"> <span id="LC71" 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;">in</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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65
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" didn't work"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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66
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#bdf1fda883543f04c4a046fdcaa8ba0db73fdb37"><strong>ebwt.h</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">@@ -126,28 +126,30 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">color</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBt2Index</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireReverse</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isBt2Index</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">EbwtParams</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">eh</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_offRate</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_color</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_entireReverse</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_color</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_entireReverse</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">eh</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_isBt2Index</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">entireReverse</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">isBt2Index</span></span><span class="p">)</span></span>
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142
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">color</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isBt2Index</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">_entireReverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">_bwtLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_len</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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147
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">_bwtSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">4</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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149
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">_lineRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineRate</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">_linesPerSide</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">_linesPerSide</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_isBt2Index</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">linesPerSide</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">_origOffRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offRate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">_offRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offRate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> <span class="n" style="color: #333;">_offMask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OFF_MASK</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_offRate</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">@@ -170,6 +172,16 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSidePairs</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">_numLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_linesPerSide</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">_ebwtTotLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSidePairs</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_sideSz</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_isBt2Index</span><span class="p">)</span> <span class="p">{</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">_sideBwtSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sideSz</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">_sideBwtLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sideBwtSz</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_bwtSz</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="n" style="color: #333;">_sideBwtSz</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="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">_sideBwtSz</span><span class="p">);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">_numSidePairs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">_numLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_linesPerSide</span><span class="p">;</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">_ebwtTotLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_sideSz</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="p">}</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"></span>
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173
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">_ebwtTotSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ebwtTotLen</span><span class="p">;</span></span>
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174
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">repOk</span><span class="p">());</span></span>
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175
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); 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="217" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -205,6 +217,7 @@ public:</td>
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205
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ebwtTotSz</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;">_ebwtTotSz</span><span class="p">;</span> <span class="p">}</span></span>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">color</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;">_color</span><span class="p">;</span> <span class="p">}</span></span>
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207
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">entireReverse</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;">_entireReverse</span><span class="p">;</span> <span class="p">}</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBt2Index</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;">_isBt2Index</span><span class="p">;</span> <span class="p">}</span></span>
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208
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"></span>
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209
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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210
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Set a new suffix-array sampling rate, which involves updating</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -238,7 +251,7 @@ public:</td>
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238
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_lineRate</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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239
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_linesPerSide</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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240
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_ftabChars</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_ebwtTotSz</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_lineSz</span><span class="p">));</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_ebwtTotSz</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">_isBt2Index</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">_lineSz</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_lineSz</span><span class="p">));</span></span>
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242
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <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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243
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"> <span class="p">}</span></span>
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244
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); 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="322" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -309,6 +322,7 @@ public:</td>
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309
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_ebwtTotSz</span><span class="p">;</span></span>
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310
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_color</span><span class="p">;</span></span>
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311
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_entireReverse</span><span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_isBt2Index</span><span class="p">;</span></span>
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312
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"><span class="p">};</span></span>
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313
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"></span>
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314
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); 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="372" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -358,6 +372,7 @@ public:</td>
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358
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _verbose(verbose), \</span></span>
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359
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _passMemExc(passMemExc), \</span></span>
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360
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _sanity(sanityCheck), \</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _isBt2Index(isBt2Index), \</span></span>
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361
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _fw(__fw), \</span></span>
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362
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _in1(NULL), \</span></span>
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363
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> _in2(NULL), \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -405,7 +420,8 @@ public:</td>
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405
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">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="LC421" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">startVerbose</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="LC422" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">passMemExc</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="LC408" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sanityCheck</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sanityCheck</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="LC424" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBt2Index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="n" style="color: #333;">Ebwt_INITS</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">Ebwt_STAT_INITS</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"> <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">@@ -468,7 +484,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">__overrideIsaRate</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"> <span class="n" style="color: #333;">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="LC486" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">passMemExc</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="LC471" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sanityCheck</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sanityCheck</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="LC488" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBt2Index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="n" style="color: #333;">Ebwt_INITS</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">Ebwt_STAT_INITS</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">_eh</span><span class="p">(</span><span class="n" style="color: #333;">joinedLen</span><span class="p">(</span><span class="n" style="color: #333;">szs</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">@@ -478,7 +495,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="c"> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">color</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;">refparams</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">REF_READ_REVERSE</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"> <span class="n" style="color: #333;">refparams</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">REF_READ_REVERSE</span><span class="p">,</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"> <span class="nb" style="color: #0086b3;">false</span> <span class="cm" style="color: #998; font-style: italic;">/* is this a bt2 index? */</span><span class="p">)</span></span>
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="c"> <span class="p">{</span></span>
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483
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef POPCNT_CAPABILITY </span></span>
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484
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">ProcessorSupport</span> <span class="n" style="color: #333;">ps</span><span class="p">;</span> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -862,7 +880,7 @@ public:</td>
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862
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ftab</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;">_ftab</span><span class="p">;</span> <span class="p">}</span></span>
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863
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">eftab</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;">_eftab</span><span class="p">;</span> <span class="p">}</span></span>
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864
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">offs</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;">_offs</span><span class="p">;</span> <span class="p">}</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32_t</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">isa</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;">_isa</span><span class="p">;</span> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* check */</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">TIndexOffU</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">isa</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;">_isa</span><span class="p">;</span> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* check */</span></span>
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866
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">plen</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;">_plen</span><span class="p">;</span> <span class="p">}</span></span>
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867
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<td class="diff-line-num new_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rstarts</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;">_rstarts</span><span class="p">;</span> <span class="p">}</span></span>
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868
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<td class="diff-line-num new_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</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;">_ebwt</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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1142,6 +1160,8 @@ public:</td>
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1142
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<td class="diff-line-num new_line" 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
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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="diff-line-num new_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">
1162
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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">mapLF</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span> <span class="n" style="color: #333;">ASSERT_ONLY</span><span class="p">(,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">overrideSanity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mapLFEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pairs</span> <span class="n" style="color: #333;">ASSERT_ONLY</span><span class="p">(,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">overrideSanity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1147
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<td class="diff-line-num new_line" 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
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mapLFEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tops</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bots</span> <span class="n" style="color: #333;">ASSERT_ONLY</span><span class="p">(,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">overrideSanity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1188,6 +1208,7 @@ public:</td>
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<td class="diff-line-num old_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1188
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<td class="diff-line-num new_line" data-linenumber="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="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_verbose</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1189
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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_passMemExc</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="diff-line-num new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_sanity</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_isBt2Index</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<td class="diff-line-num new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">_fw</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// true iff this is a forward index</span></span>
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<td class="diff-line-num old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<td class="diff-line-num new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_in1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// input fd for primary index file</span></span>
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<td class="diff-line-num old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1193
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<td class="diff-line-num new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_in2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// input fd for secondary index file</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); 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="1591" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1570,7 +1591,7 @@ struct SideLocus {</td>
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<td class="diff-line-num old_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1570
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1591
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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * from one call to initFromRow to possibly avoid a second call.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1571
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<td class="diff-line-num new_line" data-linenumber="1592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1592
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<pre style="margin: 0;"> <span id="LC1592" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1572
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<td class="diff-line-num new_line" data-linenumber="1593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1593
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<pre style="margin: 0;"> <span id="LC1593" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initFromTopBot</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">top</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1573
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<td class="diff-line-num new_line old" data-linenumber="1594" style="width: 35px; color: rgba(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="LC1573" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">bot</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1594
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">bot</span><span class="p">,</span></span>
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1574
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<td class="diff-line-num new_line" data-linenumber="1595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1595
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<pre style="margin: 0;"> <span id="LC1595" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span></span>
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1575
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1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">,</span></span>
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1576
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1597
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="c"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ltop</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1585,7 +1606,7 @@ struct SideLocus {</td>
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1585
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)(</span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spread</span><span class="p">);</span></span>
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1586
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1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_sideNum</span><span class="p">;</span></span>
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1587
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1608
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<pre style="margin: 0;"> <span id="LC1608" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span><span class="p">;</span></span>
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1588
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<pre style="margin: 0;">-<span id="LC1588" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">;</span></span>
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1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ep</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_isBt2Index</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">true</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">;</span></span>
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1589
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1610
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<pre style="margin: 0;"> <span id="LC1610" class="line" lang="c"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1590
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1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">sideBwtSz</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1591
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="c"> <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;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sideBwtSz</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1604" style="width: 35px; color: rgba(0,0,0,0.3); 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="1625" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1604,9 +1625,14 @@ struct SideLocus {</td>
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1604
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1625
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<pre style="margin: 0;"> <span id="LC1625" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideSz</span><span class="p">;</span></span>
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1605
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1626
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<pre style="margin: 0;"> <span id="LC1626" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Side length is hard-coded for now; this allows the compiler</span></span>
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1606
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1627
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// to do clever things to accelerate / and %.</span></span>
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1607
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<pre style="margin: 0;">-<span id="LC1607" class="line" lang="c"> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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1608
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<pre style="margin: 0;">-<span id="LC1608" class="line" lang="c"> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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1609
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<pre style="margin: 0;">-<span id="LC1609" class="line" lang="c"> <span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sideSz</span><span class="p">;</span></span>
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1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span><span class="p">)</span> <span class="p">{</span></span>
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1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="c"> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="c"> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1631
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1632
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="c"> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1633
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="c"> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">56</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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1634
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1635
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<pre style="margin: 0;">+<span id="LC1635" class="line" lang="c"> <span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sideSz</span><span class="p">;</span></span>
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1610
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<td class="diff-line-num new_line" data-linenumber="1636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1636
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1611
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<td class="diff-line-num new_line" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sideSz</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_ebwtTotSz</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1612
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NO_PREFETCH</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); 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="1641" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1615,7 +1641,7 @@ struct SideLocus {</td>
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1615
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1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="c"> <span class="n" style="color: #333;">PREFETCH_LOCALITY</span><span class="p">);</span></span>
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1616
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1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1617
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1643
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// prefetch this side too</span></span>
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1618
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<pre style="margin: 0;">-<span id="LC1618" class="line" lang="c"> <span class="n" style="color: #333;">_fw</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">_sideNum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</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="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// odd-numbered sides are forward</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1644
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<pre style="margin: 0;">+<span id="LC1644" class="line" lang="c"> <span class="n" style="color: #333;">_fw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ep</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_isBt2Index</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">true</span></span><span class="idiff"> </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="n" style="color: #333;"><span class="idiff">_sideNum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</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="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span>;</span> <span class="c1" style="color: #998; font-style: italic;">// odd-numbered sides are forward</span></span>
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1619
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1645
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c"> <span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// byte within side</span></span>
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1620
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1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_by</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" 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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1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="c"> <span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// bit-pair within byte</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2259" style="width: 35px; color: rgba(0,0,0,0.3); 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="2285" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2259,10 +2285,10 @@ inline void Ebwt<TStr>::countFwSideEx(const SideLocus& l, TIndexOffU* arrs) cons</td>
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2259
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="c"> <span class="n" style="color: #333;">arrs</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="p">(</span><span class="n" style="color: #333;">gt</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2260
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<td class="diff-line-num new_line" data-linenumber="2286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2286
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<pre style="margin: 0;"> <span id="LC2286" class="line" lang="c"> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">gt</span><span class="p">[</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2261
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<td class="diff-line-num new_line" data-linenumber="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2287
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<pre style="margin: 0;"> <span id="LC2287" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2262
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<td class="diff-line-num new_line old" data-linenumber="2288" style="width: 35px; color: rgba(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="LC2262" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jump<span class="idiff left right">d</span>ed into next char's section</span></span>
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2263
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<td class="diff-line-num new_line old" data-linenumber="2288" style="width: 35px; color: rgba(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="LC2263" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jump<span class="idiff left right">d</span>ed into next char's section</span></span>
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2264
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<td class="diff-line-num new_line old" data-linenumber="2288" style="width: 35px; color: rgba(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="LC2264" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jump<span class="idiff left right">d</span>ed into next char's section</span></span>
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2265
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<td class="diff-line-num new_line old" data-linenumber="2288" style="width: 35px; color: rgba(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="LC2265" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jump<span class="idiff left right">d</span>ed into next char's section</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jumped into next char's section</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jumped into next char's section</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2290
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<pre style="margin: 0;">+<span id="LC2290" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jumped into next char's section</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fchr</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]);</span> <span class="c1" style="color: #998; font-style: italic;">// can't have jumped into next char's section</span></span>
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2266
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<td class="diff-line-num new_line" data-linenumber="2292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2292
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<pre style="margin: 0;"> <span id="LC2292" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2267
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2293
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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="c"><span class="p">}</span></span>
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2268
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2294
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<pre style="margin: 0;"> <span id="LC2294" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2365,6 +2391,110 @@ inline void Ebwt<TStr>::countBwSideEx(const SideLocus& l, TIndexOffU* arrs) cons</td>
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2365
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2391
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<pre style="margin: 0;"> <span id="LC2391" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2366
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2392
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<pre style="margin: 0;"> <span id="LC2392" class="line" lang="c"><span class="p">}</span></span>
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2367
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2393
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<pre style="margin: 0;"> <span id="LC2393" class="line" lang="c"></span>
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2394
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define WITHIN_BWT_LEN(x) \</span></span>
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2395
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<pre style="margin: 0;">+<span id="LC2395" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[0], this->_eh._sideBwtLen); \</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[1], this->_eh._sideBwtLen); \</span></span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[2], this->_eh._sideBwtLen); \</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[3], this->_eh._sideBwtLen)</span></span>
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2399
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="c"></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define WITHIN_FCHR(x) \</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[0], this->fchr()[1]); \</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[1], this->fchr()[2]); \</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[2], this->fchr()[3]); \</span></span>
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2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert_leq(x[3], this->fchr()[4])</span></span>
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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="c"></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="c"><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">Ebwt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="c"> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="c"> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</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 class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span><span class="p">);</span></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="c"> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">side</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">side</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">cCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countUpTo</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">cCnt</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtLen</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">_zEbwtByteOff</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">_zEbwtByteOff</span><span class="p">)</span> <span class="p">{</span></span>
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2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Adjust for the fact that we represented $ with an 'A', but</span></span>
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2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// shouldn't count it as an 'A' here</span></span>
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2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_zEbwtByteOff</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_zEbwtByteOff</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_zEbwtBpOff</span><span class="p">))</span></span>
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2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="c"> <span class="p">{</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="c"> <span class="n" style="color: #333;">cCnt</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Adjust for '$' looking like an 'A'</span></span>
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2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="c"> <span class="p">}</span></span>
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2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="c"> <span class="p">}</span></span>
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2423
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<pre style="margin: 0;">+<span id="LC2423" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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2424
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<pre style="margin: 0;">+<span id="LC2424" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Now factor in the occ[] count at the side break</span></span>
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2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acgt8</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">side</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</span><span class="p">;</span></span>
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2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">acgt8</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2427
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_numSides</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtLen</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// b/c it's used as padding</span></span>
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2428
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<pre style="margin: 0;">+<span id="LC2428" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2429
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<pre style="margin: 0;">+<span id="LC2429" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2430
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<pre style="margin: 0;">+<span id="LC2430" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2431
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<pre style="margin: 0;">+<span id="LC2431" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cCnt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>
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2432
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<pre style="margin: 0;">+<span id="LC2432" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2433
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<pre style="margin: 0;">+<span id="LC2433" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="n" style="color: #333;">c</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;">// can't have jumpded into next char's section</span></span>
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2434
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<pre style="margin: 0;">+<span id="LC2434" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</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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2435
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<pre style="margin: 0;">+<span id="LC2435" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">cCnt</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtLen</span><span class="p">);</span></span>
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2436
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<pre style="margin: 0;">+<span id="LC2436" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2437
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<pre style="margin: 0;">+<span id="LC2437" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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2438
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<pre style="margin: 0;">+<span id="LC2438" class="line" lang="c"> <span class="p">}</span></span>
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2439
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<pre style="margin: 0;">+<span id="LC2439" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2440
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<pre style="margin: 0;">+<span id="LC2440" class="line" lang="c"> <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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2441
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<pre style="margin: 0;">+<span id="LC2441" class="line" lang="c"><span class="p">}</span></span>
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2442
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<pre style="margin: 0;">+<span id="LC2442" class="line" lang="c"></span>
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2443
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<pre style="margin: 0;">+<span id="LC2443" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2444
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<pre style="margin: 0;">+<span id="LC2444" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Count all occurrences of character c from the beginning of the</span></span>
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2445
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<pre style="margin: 0;">+<span id="LC2445" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * forward side to <by,bp> and add in the occ[] count up to the side</span></span>
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2446
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<pre style="margin: 0;">+<span id="LC2446" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * break just prior to the side.</span></span>
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2447
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<pre style="margin: 0;">+<span id="LC2447" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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2448
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<pre style="margin: 0;">+<span id="LC2448" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * A forward side is shaped like:</span></span>
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2449
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<pre style="margin: 0;">+<span id="LC2449" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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2450
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<pre style="margin: 0;">+<span id="LC2450" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * [A] [C] XXXXXXXXXXXXXXXX</span></span>
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2451
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<pre style="margin: 0;">+<span id="LC2451" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * -4- -4- --------56------ (numbers in bytes)</span></span>
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2452
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<pre style="margin: 0;">+<span id="LC2452" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * ^</span></span>
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2453
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<pre style="margin: 0;">+<span id="LC2453" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Side ptr (result from SideLocus.side())</span></span>
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2454
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<pre style="margin: 0;">+<span id="LC2454" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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2455
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<pre style="margin: 0;">+<span id="LC2455" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * And following it is a reverse side shaped like:</span></span>
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2456
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<pre style="margin: 0;">+<span id="LC2456" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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2457
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<pre style="margin: 0;">+<span id="LC2457" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * [G] [T] XXXXXXXXXXXXXXXX</span></span>
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2458
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<pre style="margin: 0;">+<span id="LC2458" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * -4- -4- --------56------ (numbers in bytes)</span></span>
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2459
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<pre style="margin: 0;">+<span id="LC2459" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * ^</span></span>
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2460
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<pre style="margin: 0;">+<span id="LC2460" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Side ptr (result from SideLocus.side())</span></span>
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2461
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<pre style="margin: 0;">+<span id="LC2461" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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2463
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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="c"><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span></span>
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2464
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<pre style="margin: 0;">+<span id="LC2464" class="line" lang="c"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Ebwt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arrs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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2465
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<pre style="margin: 0;">+<span id="LC2465" class="line" lang="c"> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</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 class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span><span class="p">);</span></span>
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2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="c"> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span><span class="p">);</span></span>
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2467
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<pre style="margin: 0;">+<span id="LC2467" class="line" lang="c"> <span class="n" style="color: #333;">countUpToEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">);</span></span>
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2468
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<pre style="margin: 0;">+<span id="LC2468" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">_zEbwtByteOff</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">_zEbwtByteOff</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2469
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<pre style="margin: 0;">+<span id="LC2469" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Adjust for the fact that we represented $ with an 'A', but</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2470
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<pre style="margin: 0;">+<span id="LC2470" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// shouldn't count it as an 'A' here</span></span>
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2471
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<pre style="margin: 0;">+<span id="LC2471" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_zEbwtByteOff</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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2472
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<pre style="margin: 0;">+<span id="LC2472" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_zEbwtByteOff</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_zEbwtBpOff</span><span class="p">))</span></span>
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2473
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<pre style="margin: 0;">+<span id="LC2473" class="line" lang="c"> <span class="p">{</span></span>
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2474
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<pre style="margin: 0;">+<span id="LC2474" class="line" lang="c"> <span class="n" style="color: #333;">arrs</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="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Adjust for '$' looking like an 'A'</span></span>
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2475
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<pre style="margin: 0;">+<span id="LC2475" class="line" lang="c"> <span class="p">}</span></span>
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2476
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<pre style="margin: 0;">+<span id="LC2476" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2477" class="line" lang="c"> <span class="n" style="color: #333;">WITHIN_FCHR</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="c"> <span class="n" style="color: #333;">WITHIN_BWT_LEN</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2479" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Now factor in the occ[] count at the side break</span></span>
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">side</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">side</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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2481
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<pre style="margin: 0;">+<span id="LC2481" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acgt16</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">side</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_sideSz</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">OFF_SIZE</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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2482
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<pre style="margin: 0;">+<span id="LC2482" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">acgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">acgt16</span><span class="p">);</span></span>
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2483
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<pre style="margin: 0;">+<span id="LC2483" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">sideBwtLen</span><span class="p">());</span></span>
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2484
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<pre style="margin: 0;">+<span id="LC2484" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</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="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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2485
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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2487
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<pre style="margin: 0;">+<span id="LC2487" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">sideBwtLen</span><span class="p">());</span></span>
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2488
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<pre style="margin: 0;">+<span id="LC2488" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2489
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<pre style="margin: 0;">+<span id="LC2489" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2490
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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2491
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<pre style="margin: 0;">+<span id="LC2491" class="line" lang="c"> <span class="n" style="color: #333;">arrs</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="p">(</span><span class="n" style="color: #333;">acgt</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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2492
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<pre style="margin: 0;">+<span id="LC2492" class="line" lang="c"> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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2493
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<pre style="margin: 0;">+<span id="LC2493" class="line" lang="c"> <span class="n" style="color: #333;">arrs</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="p">(</span><span class="n" style="color: #333;">acgt</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="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2494
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<pre style="margin: 0;">+<span id="LC2494" class="line" lang="c"> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fchr</span><span class="p">()[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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2495
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<pre style="margin: 0;">+<span id="LC2495" class="line" lang="c"> <span class="n" style="color: #333;">WITHIN_FCHR</span><span class="p">(</span><span class="n" style="color: #333;">arrs</span><span class="p">);</span></span>
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2496
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<pre style="margin: 0;">+<span id="LC2496" class="line" lang="c"><span class="p">}</span></span>
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2497
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<pre style="margin: 0;">+<span id="LC2497" class="line" lang="c"></span>
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2368
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2498
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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2369
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2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Given top and bot loci, calculate counts of all four DNA chars up to</span></span>
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2370
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2500
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<pre style="margin: 0;"> <span id="LC2500" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * those loci. Used for more advanced backtracking-search.</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="2516" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2386,10 +2516,21 @@ inline void Ebwt<TStr>::mapLFEx(const SideLocus& ltop,</td>
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2386
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2516
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<pre style="margin: 0;"> <span id="LC2516" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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2387
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2517
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<pre style="margin: 0;"> <span id="LC2517" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2388
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2518
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<pre style="margin: 0;"> <span id="LC2518" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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2389
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<pre style="margin: 0;">-<span id="LC2389" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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2390
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<td class="diff-line-num new_line old" data-linenumber="2519" style="width: 35px; color: rgba(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="LC2390" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2391
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<td class="diff-line-num new_line old" data-linenumber="2519" style="width: 35px; color: rgba(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="LC2391" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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2392
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<td class="diff-line-num new_line old" data-linenumber="2519" style="width: 35px; color: rgba(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="LC2392" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2519
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<pre style="margin: 0;">+<span id="LC2519" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2520
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<pre style="margin: 0;">+<span id="LC2520" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2521
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<pre style="margin: 0;">+<span id="LC2521" class="line" lang="c"> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">)</span></span>
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2522
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<pre style="margin: 0;">+<span id="LC2522" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2523
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<pre style="margin: 0;">+<span id="LC2523" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2524
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<pre style="margin: 0;">+<span id="LC2524" class="line" lang="c"> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2525
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<pre style="margin: 0;">+<span id="LC2525" class="line" lang="c"> <span class="p">}</span></span>
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2526
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<pre style="margin: 0;">+<span id="LC2526" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2527
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<pre style="margin: 0;">+<span id="LC2527" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2528
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<pre style="margin: 0;">+<span id="LC2528" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2529
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<pre style="margin: 0;">+<span id="LC2529" class="line" lang="c"> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2530
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<pre style="margin: 0;">+<span id="LC2530" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2531
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<pre style="margin: 0;">+<span id="LC2531" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2532
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<pre style="margin: 0;">+<span id="LC2532" class="line" lang="c"> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2533
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<pre style="margin: 0;">+<span id="LC2533" class="line" lang="c"> <span class="p">}</span></span>
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2393
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2534
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<pre style="margin: 0;"> <span id="LC2534" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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<td class="diff-line-num old_line" data-linenumber="2394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2394
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<td class="diff-line-num new_line" data-linenumber="2535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2535
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<pre style="margin: 0;"> <span id="LC2535" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2395
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<td class="diff-line-num new_line" data-linenumber="2536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2536
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<pre style="margin: 0;"> <span id="LC2536" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Make sure results match up with individual calls to mapLF;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2422" style="width: 35px; color: rgba(0,0,0,0.3); 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="2563" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2422,8 +2563,13 @@ inline void Ebwt<TStr>::mapLFEx(const SideLocus& l,</td>
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2422
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2563
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<pre style="margin: 0;"> <span id="LC2563" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2423
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<td class="diff-line-num new_line" data-linenumber="2564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2564
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<pre style="margin: 0;"> <span id="LC2564" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2424
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<td class="diff-line-num new_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2565
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<pre style="margin: 0;"> <span id="LC2565" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2425
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<td class="diff-line-num new_line old" data-linenumber="2566" style="width: 35px; color: rgba(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="LC2425" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2426
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<td class="diff-line-num new_line old" data-linenumber="2566" style="width: 35px; color: rgba(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="LC2426" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2566
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<pre style="margin: 0;">+<span id="LC2566" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2567
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<pre style="margin: 0;">+<span id="LC2567" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2568
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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="c"> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">);</span></span>
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2570
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<pre style="margin: 0;">+<span id="LC2570" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2571
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<pre style="margin: 0;">+<span id="LC2571" class="line" lang="c"> <span class="n" style="color: #333;">countBwSideEx</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">arrs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2572
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<pre style="margin: 0;">+<span id="LC2572" class="line" lang="c"> <span class="p">}</span></span>
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2427
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<td class="diff-line-num new_line" data-linenumber="2573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2573
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<pre style="margin: 0;"> <span id="LC2573" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2428
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2574
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<pre style="margin: 0;"> <span id="LC2574" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</span><span class="p">)</span> <span class="p">{</span></span>
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2429
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2575
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<pre style="margin: 0;"> <span id="LC2575" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Make sure results match up with individual calls to mapLF;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); 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="2600" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2454,8 +2600,14 @@ inline TIndexOffU Ebwt<TStr>::mapLF(const SideLocus& l</td>
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2454
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2600
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<pre style="margin: 0;"> <span id="LC2600" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rowL</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2455
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2601
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<pre style="margin: 0;"> <span id="LC2601" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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2456
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2602
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<pre style="margin: 0;"> <span id="LC2602" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2457
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<td class="diff-line-num new_line old" data-linenumber="2603" style="width: 35px; color: rgba(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="LC2457" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2458
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<td class="diff-line-num new_line old" data-linenumber="2603" style="width: 35px; color: rgba(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="LC2458" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2603
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<pre style="margin: 0;">+<span id="LC2603" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2604
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<pre style="margin: 0;">+<span id="LC2604" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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2605
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<pre style="margin: 0;">+<span id="LC2605" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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2606
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<pre style="margin: 0;">+<span id="LC2606" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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2607
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<pre style="margin: 0;">+<span id="LC2607" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2608
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<pre style="margin: 0;">+<span id="LC2608" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2609
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<pre style="margin: 0;">+<span id="LC2609" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2610
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<pre style="margin: 0;">+<span id="LC2610" class="line" lang="c"> <span class="p">}</span></span>
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2459
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<td class="diff-line-num new_line" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2611
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<pre style="margin: 0;"> <span id="LC2611" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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2460
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<td class="diff-line-num new_line" data-linenumber="2612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2612
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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2461
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<td class="diff-line-num new_line" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2613
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<pre style="margin: 0;"> <span id="LC2613" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</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="2485" style="width: 35px; color: rgba(0,0,0,0.3); 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="2637" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2485,8 +2637,14 @@ inline TIndexOffU Ebwt<TStr>::mapLF(const SideLocus& l, int c</td>
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2485
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<td class="diff-line-num new_line" data-linenumber="2637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2637
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<pre style="margin: 0;"> <span id="LC2637" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2486
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<td class="diff-line-num new_line" data-linenumber="2638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2638
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<pre style="margin: 0;"> <span id="LC2638" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2487
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<td class="diff-line-num new_line" data-linenumber="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2639
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<pre style="margin: 0;"> <span id="LC2639" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2488
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<td class="diff-line-num new_line old" data-linenumber="2640" style="width: 35px; color: rgba(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="LC2488" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2489
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<td class="diff-line-num new_line old" data-linenumber="2640" style="width: 35px; color: rgba(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="LC2489" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2640
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<pre style="margin: 0;">+<span id="LC2640" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2641
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<pre style="margin: 0;">+<span id="LC2641" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2642
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<pre style="margin: 0;">+<span id="LC2642" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2643
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<pre style="margin: 0;">+<span id="LC2643" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2644
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<pre style="margin: 0;">+<span id="LC2644" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2645
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<pre style="margin: 0;">+<span id="LC2645" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2646
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<pre style="margin: 0;">+<span id="LC2646" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2647
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<pre style="margin: 0;">+<span id="LC2647" class="line" lang="c"> <span class="p">}</span></span>
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2490
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<td class="diff-line-num new_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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2491
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<td class="diff-line-num new_line" data-linenumber="2649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2492
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2650
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<pre style="margin: 0;"> <span id="LC2650" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</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="2517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2517,8 +2675,13 @@ inline TIndexOffU Ebwt<TStr>::mapLF1(TIndexOffU row, const SideLocus& l, int c</td>
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2517
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2675
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<pre style="margin: 0;"> <span id="LC2675" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2518
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<td class="diff-line-num new_line" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2676
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<pre style="margin: 0;"> <span id="LC2676" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
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<td class="diff-line-num new_line" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2677
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<pre style="margin: 0;"> <span id="LC2677" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2520
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<td class="diff-line-num new_line old" data-linenumber="2678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2520" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2521
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<td class="diff-line-num new_line old" data-linenumber="2678" style="width: 35px; color: rgba(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="LC2521" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2678
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<pre style="margin: 0;">+<span id="LC2678" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2679
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<pre style="margin: 0;">+<span id="LC2679" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2680
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<pre style="margin: 0;">+<span id="LC2680" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2681
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<pre style="margin: 0;">+<span id="LC2681" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2682
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<pre style="margin: 0;">+<span id="LC2682" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2683
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<pre style="margin: 0;">+<span id="LC2683" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2684
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<pre style="margin: 0;">+<span id="LC2684" class="line" lang="c"> <span class="p">}</span></span>
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2522
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<td class="diff-line-num new_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2685
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<pre style="margin: 0;"> <span id="LC2685" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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2523
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2686
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<pre style="margin: 0;"> <span id="LC2686" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2524
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<td class="diff-line-num new_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2687
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<pre style="margin: 0;"> <span id="LC2687" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</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="2549" style="width: 35px; color: rgba(0,0,0,0.3); 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="2712" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2549,8 +2712,13 @@ inline int Ebwt<TStr>::mapLF1(TIndexOffU& row, const SideLocus& l</td>
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2549
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<td class="diff-line-num new_line" data-linenumber="2712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2712
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<pre style="margin: 0;"> <span id="LC2712" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rowL</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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2550
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<td class="diff-line-num new_line" data-linenumber="2713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2713
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<pre style="margin: 0;"> <span id="LC2713" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2551
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<td class="diff-line-num new_line" data-linenumber="2714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2714
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<pre style="margin: 0;"> <span id="LC2714" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2552
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<td class="diff-line-num new_line old" data-linenumber="2715" style="width: 35px; color: rgba(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="LC2552" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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2553
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<td class="diff-line-num new_line old" data-linenumber="2715" style="width: 35px; color: rgba(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="LC2553" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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2715
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<pre style="margin: 0;">+<span id="LC2715" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2716
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<pre style="margin: 0;">+<span id="LC2716" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2717
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<pre style="margin: 0;">+<span id="LC2717" class="line" lang="c"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2718
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<pre style="margin: 0;">+<span id="LC2718" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2719
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<pre style="margin: 0;">+<span id="LC2719" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2720
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<pre style="margin: 0;">+<span id="LC2720" class="line" lang="c"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2721
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<pre style="margin: 0;">+<span id="LC2721" class="line" lang="c"> <span class="p">}</span></span>
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2554
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<td class="diff-line-num new_line" data-linenumber="2722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2722
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<pre style="margin: 0;"> <span id="LC2722" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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2555
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<td class="diff-line-num new_line" data-linenumber="2723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2723
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<pre style="margin: 0;"> <span id="LC2723" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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2556
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<td class="diff-line-num new_line" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2724
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<pre style="margin: 0;"> <span id="LC2724" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_sanity</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overrideSanity</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="2829" style="width: 35px; color: rgba(0,0,0,0.3); 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="2997" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2829,8 +2997,13 @@ inline bool Ebwt<TStr>::reportReconstruct(const String<Dna5>& query,</td>
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2829
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<td class="diff-line-num new_line" data-linenumber="2997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2997
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<pre style="margin: 0;"> <span id="LC2997" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span></span>
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2830
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<td class="diff-line-num new_line" data-linenumber="2998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2998
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<pre style="margin: 0;"> <span id="LC2998" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2831
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<td class="diff-line-num new_line" data-linenumber="2999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2999
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<pre style="margin: 0;"> <span id="LC2999" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2832
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<td class="diff-line-num new_line old" data-linenumber="3000" style="width: 35px; color: rgba(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="LC2832" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2833
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<td class="diff-line-num new_line old" data-linenumber="3000" style="width: 35px; color: rgba(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="LC2833" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3000
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<pre style="margin: 0;">+<span id="LC3000" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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3001
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<pre style="margin: 0;">+<span id="LC3001" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3002
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<pre style="margin: 0;">+<span id="LC3002" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3003
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<pre style="margin: 0;">+<span id="LC3003" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3004
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<pre style="margin: 0;">+<span id="LC3004" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3005
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<pre style="margin: 0;">+<span id="LC3005" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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3006
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<pre style="margin: 0;">+<span id="LC3006" class="line" lang="c"> <span class="p">}</span></span>
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2834
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<td class="diff-line-num new_line" data-linenumber="3007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3007
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<pre style="margin: 0;"> <span id="LC3007" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2835
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3008
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<pre style="margin: 0;"> <span id="LC3008" class="line" lang="c"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2836
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3009
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<pre style="margin: 0;"> <span id="LC3009" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// update row</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2883,8 +3056,13 @@ inline bool Ebwt<TStr>::reportReconstruct(const String<Dna5>& query,</td>
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2883
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3056
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<pre style="margin: 0;"> <span id="LC3056" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2884
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<td class="diff-line-num new_line" data-linenumber="3057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3057
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<pre style="margin: 0;"> <span id="LC3057" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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2885
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<td class="diff-line-num new_line" data-linenumber="3058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3058
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<pre style="margin: 0;"> <span id="LC3058" class="line" lang="c"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2886
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC2886" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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2887
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC2887" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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3059
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<pre style="margin: 0;">+<span id="LC3059" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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3060
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<pre style="margin: 0;">+<span id="LC3060" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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3061
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<pre style="margin: 0;">+<span id="LC3061" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3062" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3063" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3064
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<pre style="margin: 0;">+<span id="LC3064" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3065
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<pre style="margin: 0;">+<span id="LC3065" class="line" lang="c"> <span class="p">}</span></span>
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2888
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<td class="diff-line-num new_line" data-linenumber="3066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3066
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<pre style="margin: 0;"> <span id="LC3066" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2889
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<td class="diff-line-num new_line" data-linenumber="3067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3067
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<pre style="margin: 0;"> <span id="LC3067" class="line" lang="c"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2890
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<td class="diff-line-num new_line" data-linenumber="3068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3068
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<pre style="margin: 0;"> <span id="LC3068" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// update row</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2922" style="width: 35px; color: rgba(0,0,0,0.3); 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="3100" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2922,8 +3100,14 @@ inline bool Ebwt<TStr>::reportReconstruct(const String<Dna5>& query,</td>
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2922
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<td class="diff-line-num new_line" data-linenumber="3100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3100
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<pre style="margin: 0;"> <span id="LC3100" class="line" lang="c"> <span class="n" style="color: #333;">appendValue</span><span class="p">(</span><span class="n" style="color: #333;">rbuf</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">Dna5</span><span class="p">)</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2923
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<td class="diff-line-num new_line" 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
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<pre style="margin: 0;"> <span id="LC3101" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2924
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<td class="diff-line-num new_line" data-linenumber="3102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3102
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<pre style="margin: 0;"> <span id="LC3102" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2925
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC2925" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2926
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC2926" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3103
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<pre style="margin: 0;">+<span id="LC3103" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fw</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3104
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<pre style="margin: 0;">+<span id="LC3104" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Forward side</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3105" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_isBt2Index</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">countFwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3106" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">countBt2Side</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3107" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3108" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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
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<pre style="margin: 0;">+<span id="LC3109" class="line" lang="c"> <span class="n" style="color: #333;">newi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countBwSide</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Backward side</span></span>
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<td class="diff-line-num new new_line" 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
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<pre style="margin: 0;">+<span id="LC3110" class="line" lang="c"> <span class="p">}</span></span>
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2927
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<td class="diff-line-num new_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3111
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<pre style="margin: 0;"> <span id="LC3111" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2928
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<td class="diff-line-num new_line" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3112
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<pre style="margin: 0;"> <span id="LC3112" class="line" lang="c"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">newi</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2929
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3113
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<pre style="margin: 0;"> <span id="LC3113" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newi</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// update row</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3208" style="width: 35px; color: rgba(0,0,0,0.3); 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="3392" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3208,11 +3392,11 @@ void Ebwt<TStr>::readIntoMemory(</td>
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3208
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3392
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<pre style="margin: 0;"> <span id="LC3392" class="line" lang="c"> <span class="n" style="color: #333;">EbwtParams</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eh</span><span class="p">;</span></span>
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3209
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3393
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<pre style="margin: 0;"> <span id="LC3393" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">deleteEh</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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<td class="diff-line-num old_line" data-linenumber="3210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3210
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<td class="diff-line-num new_line" data-linenumber="3394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3394
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<pre style="margin: 0;"> <span id="LC3394" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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3211
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<pre style="margin: 0;">-<span id="LC3211" class="line" lang="c"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireRev</span><span class="p">);</span></span>
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3395
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<pre style="margin: 0;">+<span id="LC3395" class="line" lang="c"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireRev</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_isBt2Index</span></span><span class="p">);</span></span>
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3212
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<td class="diff-line-num new_line" data-linenumber="3396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3396
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<pre style="margin: 0;"> <span id="LC3396" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_verbose</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">startVerbose</span><span class="p">)</span> <span class="n" style="color: #333;">params</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;">cerr</span><span class="p">);</span></span>
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3213
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3397
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<pre style="margin: 0;"> <span id="LC3397" class="line" lang="c"> <span class="n" style="color: #333;">eh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">;</span></span>
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3214
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3398
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<pre style="margin: 0;"> <span id="LC3398" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3215
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<pre style="margin: 0;">-<span id="LC3215" class="line" lang="c"> <span class="n" style="color: #333;">eh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">EbwtParams</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireRev</span><span class="p">);</span></span>
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3399
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<pre style="margin: 0;">+<span id="LC3399" class="line" lang="c"> <span class="n" style="color: #333;">eh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">EbwtParams</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</span><span class="p">,</span> <span class="n" style="color: #333;">isaRate</span><span class="p">,</span> <span class="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireRev</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_isBt2Index</span></span><span class="p">);</span></span>
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3216
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3400
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<pre style="margin: 0;"> <span id="LC3400" class="line" lang="c"> <span class="n" style="color: #333;">deleteEh</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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3217
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3401
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<pre style="margin: 0;"> <span id="LC3401" class="line" lang="c"> <span class="p">}</span></span>
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3218
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3402
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<pre style="margin: 0;"> <span id="LC3402" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3678" style="width: 35px; color: rgba(0,0,0,0.3); 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="3862" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3678,6 +3862,7 @@ void Ebwt<TStr>::readIntoMemory(</td>
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3678
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3862
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<pre style="margin: 0;"> <span id="LC3862" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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3679
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3863
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<pre style="margin: 0;"> <span id="LC3863" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Read reference names from an input stream 'in' for an Ebwt primary</span></span>
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3680
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3864
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<pre style="margin: 0;"> <span id="LC3864" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * file and store them in 'refnames'.</span></span>
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3865
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<pre style="margin: 0;">+<span id="LC3865" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * TODO: revisit this function</span></span>
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3681
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3866
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<pre style="margin: 0;"> <span id="LC3866" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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3682
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<pre style="margin: 0;"> <span id="LC3867" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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3683
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3868
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<pre style="margin: 0;"> <span id="LC3868" class="line" lang="c"><span class="n" style="color: #333;">readEbwtRefnames</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="n" style="color: #333;">vector</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;">refnames</span><span class="p">)</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">@@ -3710,7 +3895,11 @@ readEbwtRefnames(FILE* fin, vector<string>& refnames) {</td>
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3710
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3895
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<pre style="margin: 0;"> <span id="LC3895" class="line" lang="c"> <span class="p">}</span></span>
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3711
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3896
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<pre style="margin: 0;"> <span id="LC3896" class="line" lang="c"></span>
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3712
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3897
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<pre style="margin: 0;"> <span id="LC3897" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Create a new EbwtParams from the entries read from primary stream</span></span>
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3713
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<pre style="margin: 0;">-<span id="LC3713" class="line" lang="c"> <span class="n" style="color: #333;">EbwtParams</span> <span class="n" style="color: #333;">eh</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</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="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">);</span></span>
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3898
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<pre style="margin: 0;">+<span id="LC3898" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isBt2Index</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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3899
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<pre style="margin: 0;">+<span id="LC3899" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bt2"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bt2"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3900" class="line" lang="c"> <span class="n" style="color: #333;">isBt2Index</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="LC3901" class="line" lang="c"> <span class="p">}</span></span>
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3902
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<pre style="margin: 0;">+<span id="LC3902" class="line" lang="c"> <span class="n" style="color: #333;">EbwtParams</span> <span class="n" style="color: #333;">eh</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">lineRate</span><span class="p">,</span> <span class="n" style="color: #333;">linesPerSide</span><span class="p">,</span> <span class="n" style="color: #333;">offRate</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="n" style="color: #333;">ftabChars</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">entireReverse</span><span class="p">,</span> <span class="n" style="color: #333;">isBt2Index</span><span class="p">);</span></span>
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3714
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3903
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<pre style="margin: 0;"> <span id="LC3903" class="line" lang="c"></span>
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3715
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3904
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<pre style="margin: 0;"> <span id="LC3904" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">nPat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readI</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="n" style="color: #333;">switchEndian</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// nPat</span></span>
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3716
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3905
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<pre style="margin: 0;"> <span id="LC3905" class="line" lang="c"> <span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="n" style="color: #333;">nPat</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#3b01777a95af313429e4b310e9c1f9f64244744b"><strong>ebwt_build.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">@@ -333,12 +333,22 @@ static void driver(const string& infile,</td>
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<pre style="margin: 0;"> <span id="LC333" 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="LC334" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Adapt sequence files to ifstreams</span></span>
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<pre style="margin: 0;"> <span id="LC335" 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;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">infiles</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 class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: could not open "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">infiles</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">FileBuf</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FileBuf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isGzippedFile</span><span class="p">(</span><span class="n" style="color: #333;">infiles</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 class="p">{</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">zFp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">infiles</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 class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zFp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="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;">"Error: could not open "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">infiles</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 class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileBuf</span><span class="p">(</span><span class="n" style="color: #333;">zFp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" 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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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">infiles</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 class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: could not open "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">infiles</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileBuf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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340
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">FileBuf</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileBuf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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342
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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343
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fb</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</span><span class="p">());</span></span>
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344
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">fb</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -472,7 +482,8 @@ static void driver(const string& infile,</td>
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472
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"> <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;">// override isaRate</span></span>
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473
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// be talkative</span></span>
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474
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">autoMem</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// pass exceptions up to the toplevel so that we can adjust memory settings automatically</span></span>
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475
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// verify results and internal consistency</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// verify results and internal consistency</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// are we building a bt2 index?</span></span>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Note that the Ebwt is *not* resident in memory at this time. To</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// load it into memory, call ebwt.loadIntoMemory()</span></span>
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478
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<li id="325e44ac9e9631edc4f328e8eaa8247f8faaa318">
<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#325e44ac9e9631edc4f328e8eaa8247f8faaa318"><strong>ebwt_search.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">@@ -480,6 +480,9 @@ static void printUsage(ostream& out) {</td>
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480
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Input:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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481
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -q query input files are FASTQ .fq/.fastq (default)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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482
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -f query input files are (multi-)FASTA .fa/.mfa"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -F k:<int>,i:<int> query input files are continuous FASTA where reads"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" are substrings (k-mers) extracted from a FASTA file <s>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" and aligned at offsets 1, 1+i, 1+2i ... end of reference"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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483
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -r query input files are raw one-sequence-per-line"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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484
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -c query sequences given on cmd line (as <mates>, <singles>)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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485
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -C reads and index are in colorspace"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1459,8 +1462,7 @@ static void exactSearch(PatternComposer& _patsrc,</td>
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1459
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1462
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<pre style="margin: 0;"> <span id="LC1462" 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;">refs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loaded</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1460
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1463
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<pre style="margin: 0;"> <span id="LC1463" class="line" lang="cpp"> <span class="p">}</span></span>
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1461
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<td class="diff-line-num new_line" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="cpp"> <span class="n" style="color: #333;">exactSearch_refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</span><span class="p">;</span></span>
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1462
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<pre style="margin: 0;">-<span id="LC1462" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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1463
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<pre style="margin: 0;">-<span id="LC1463" class="line" lang="cpp"> <span class="n" style="color: #333;">tids</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">));</span></span>
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1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tids</span><span class="p">[</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">)];</span></span>
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1464
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1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITH_TBB</span></span>
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1465
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1467
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<pre style="margin: 0;"> <span id="LC1467" class="line" lang="cpp"> <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="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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1466
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1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">thread_tracking_pair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tps</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); 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="1569" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1567,10 +1569,9 @@ static void exactSearch(PatternComposer& _patsrc,</td>
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1567
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="cpp"> <span class="n" style="color: #333;">SLEEP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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1568
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1570
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="cpp"> <span class="p">}</span></span>
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1569
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1571
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1570
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<pre style="margin: 0;">-<span id="LC1570" 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;">nthreads</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 class="p">{</span></span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" 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;">nthreads</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></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 class="p">{</span></span>
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1571
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1573
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="cpp"> <span class="p">}</span></span>
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1573
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<pre style="margin: 0;">-<span id="LC1573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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1575
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<pre style="margin: 0;"> <span id="LC1575" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1576
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="cpp"></span>
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1577
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<pre style="margin: 0;"> <span id="LC1577" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _WIN32</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1844" style="width: 35px; color: rgba(0,0,0,0.3); 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="1845" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1844,8 +1845,7 @@ static void mismatchSearchFull(PatternComposer& _patsrc,</td>
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1844
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1845
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<pre style="margin: 0;"> <span id="LC1845" class="line" lang="cpp"> <span class="p">}</span></span>
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1846
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="cpp"> <span class="n" style="color: #333;">mismatchSearch_refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</span><span class="p">;</span></span>
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1847
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<pre style="margin: 0;"> <span id="LC1847" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1847" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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1848
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<pre style="margin: 0;">-<span id="LC1848" class="line" lang="cpp"> <span class="n" style="color: #333;">tids</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1848" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tids</span><span class="p">[</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">)];</span></span>
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<pre style="margin: 0;"> <span id="LC1849" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITH_TBB</span></span>
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<pre style="margin: 0;"> <span id="LC1850" class="line" lang="cpp"> <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="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1851" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">thread_tracking_pair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tps</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1953,10 +1953,9 @@ static void mismatchSearchFull(PatternComposer& _patsrc,</td>
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1953
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1953
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<pre style="margin: 0;"> <span id="LC1953" class="line" lang="cpp"> <span class="n" style="color: #333;">SLEEP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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1954
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1954
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<pre style="margin: 0;"> <span id="LC1954" class="line" lang="cpp"> <span class="p">}</span></span>
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1955
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1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1956
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<pre style="margin: 0;">-<span id="LC1956" 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;">nthreads</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 class="p">{</span></span>
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1956
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<pre style="margin: 0;">+<span id="LC1956" 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;">nthreads</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></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 class="p">{</span></span>
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1957
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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1958
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1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="cpp"> <span class="p">}</span></span>
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1959
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<pre style="margin: 0;">-<span id="LC1959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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1960
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1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1961
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1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="cpp"></span>
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1962
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1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _WIN32</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); 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="2348" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2349,8 +2348,7 @@ static void twoOrThreeMismatchSearchFull(</td>
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2349
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2348
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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="cpp"> <span class="n" style="color: #333;">twoOrThreeMismatchSearch_hitMask</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2350
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2349
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<pre style="margin: 0;"> <span id="LC2349" class="line" lang="cpp"> <span class="n" style="color: #333;">twoOrThreeMismatchSearch_two</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two</span><span class="p">;</span></span>
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2351
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2350
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<pre style="margin: 0;"> <span id="LC2350" class="line" lang="cpp"></span>
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2352
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<pre style="margin: 0;">-<span id="LC2352" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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2353
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<pre style="margin: 0;">-<span id="LC2353" class="line" lang="cpp"> <span class="n" style="color: #333;">tids</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tids</span><span class="p">[</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">)];</span></span>
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2354
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2352
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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITH_TBB</span></span>
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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="cpp"> <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="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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2356
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2354
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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">thread_tracking_pair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tps</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); 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="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2458,10 +2456,9 @@ static void twoOrThreeMismatchSearchFull(</td>
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2458
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2456
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<pre style="margin: 0;"> <span id="LC2456" class="line" lang="cpp"> <span class="n" style="color: #333;">SLEEP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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2459
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2457
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<pre style="margin: 0;"> <span id="LC2457" class="line" lang="cpp"> <span class="p">}</span></span>
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2460
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2458
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<pre style="margin: 0;"> <span id="LC2458" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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2461
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<pre style="margin: 0;">-<span id="LC2461" 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;">nthreads</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 class="p">{</span></span>
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2459
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<pre style="margin: 0;">+<span id="LC2459" 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;">nthreads</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></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 class="p">{</span></span>
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2462
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2460
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<pre style="margin: 0;"> <span id="LC2460" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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2463
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2461
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<pre style="margin: 0;"> <span id="LC2461" class="line" lang="cpp"> <span class="p">}</span></span>
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2464
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<pre style="margin: 0;">-<span id="LC2464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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2465
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2462
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<pre style="margin: 0;"> <span id="LC2462" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2466
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2463
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<pre style="margin: 0;"> <span id="LC2463" class="line" lang="cpp"></span>
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2467
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2464
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<pre style="margin: 0;"> <span id="LC2464" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _WIN32</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2898" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2901,8 +2898,7 @@ static void seededQualCutoffSearchFull(</td>
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2901
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2898
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<pre style="margin: 0;"> <span id="LC2898" class="line" lang="cpp"> <span class="p">}</span></span>
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2902
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2899
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<pre style="margin: 0;"> <span id="LC2899" class="line" lang="cpp"> <span class="n" style="color: #333;">seededQualSearch_refs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refs</span><span class="p">;</span></span>
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2903
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2900
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<pre style="margin: 0;"> <span id="LC2900" class="line" lang="cpp"></span>
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2904
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<pre style="margin: 0;">-<span id="LC2904" class="line" lang="cpp"> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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2905
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<pre style="margin: 0;">-<span id="LC2905" class="line" lang="cpp"> <span class="n" style="color: #333;">tids</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC2901" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tids</span><span class="p">[</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">thread_ceiling</span><span class="p">)];</span></span>
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2906
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2902
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<pre style="margin: 0;"> <span id="LC2902" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef WITH_TBB</span></span>
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2907
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2903
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<pre style="margin: 0;"> <span id="LC2903" class="line" lang="cpp"> <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="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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2908
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2904
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<pre style="margin: 0;"> <span id="LC2904" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">thread_tracking_pair</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tps</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3018" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3018,10 +3014,9 @@ static void seededQualCutoffSearchFull(</td>
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3018
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3014
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<pre style="margin: 0;"> <span id="LC3014" class="line" lang="cpp"> <span class="n" style="color: #333;">SLEEP</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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3019
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3015
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<pre style="margin: 0;"> <span id="LC3015" class="line" lang="cpp"> <span class="p">}</span></span>
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3020
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3016
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<pre style="margin: 0;"> <span id="LC3016" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3021
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC3021" 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;">nthreads</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 class="p">{</span></span>
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3017
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<pre style="margin: 0;">+<span id="LC3017" 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;">nthreads</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></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 class="p">{</span></span>
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3022
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3018
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<pre style="margin: 0;"> <span id="LC3018" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="3023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3023
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3019
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<pre style="margin: 0;"> <span id="LC3019" class="line" lang="cpp"> <span class="p">}</span></span>
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3024
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<pre style="margin: 0;">-<span id="LC3024" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">tids</span><span class="p">;</span></span>
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3025
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3020
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<pre style="margin: 0;"> <span id="LC3020" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3026
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3021
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<pre style="margin: 0;"> <span id="LC3021" class="line" lang="cpp"></span>
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3027
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3022
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<pre style="margin: 0;"> <span id="LC3022" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _WIN32</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3127,6 +3122,11 @@ static void driver(const char * type,</td>
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3127
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3122
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<pre style="margin: 0;"> <span id="LC3122" class="line" lang="cpp"> <span class="p">}</span></span>
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3128
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3123
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<pre style="margin: 0;"> <span id="LC3123" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Adjust</span></span>
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3129
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3124
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<pre style="margin: 0;"> <span id="LC3124" class="line" lang="cpp"> <span class="n" style="color: #333;">adjustedEbwtFileBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustEbwtBase</span><span class="p">(</span><span class="n" style="color: #333;">argv0</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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3125
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<pre style="margin: 0;">+<span id="LC3125" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isBt2Index</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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3126
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<pre style="margin: 0;">+<span id="LC3126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bt2"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bt2l"</span><span class="p">)</span> <span class="p">{</span></span>
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3127
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<pre style="margin: 0;">+<span id="LC3127" class="line" lang="cpp"> <span class="n" style="color: #333;">isBt2Index</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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3128
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<pre style="margin: 0;">+<span id="LC3128" class="line" lang="cpp"> <span class="p">}</span></span>
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3129
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<pre style="margin: 0;">+<span id="LC3129" class="line" lang="cpp"></span>
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3130
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3130
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<pre style="margin: 0;"> <span id="LC3130" class="line" lang="cpp"></span>
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3131
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3131
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<pre style="margin: 0;"> <span id="LC3131" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">patsrcs_a</span><span class="p">;</span></span>
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3132
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3132
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<pre style="margin: 0;"> <span id="LC3132" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">PatternSource</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">patsrcs_b</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); 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="3266" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3266,7 +3266,8 @@ static void driver(const char * type,</td>
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3266
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3266
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<pre style="margin: 0;"> <span id="LC3266" class="line" lang="cpp"> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// whether to be talkative</span></span>
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3267
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3267
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<pre style="margin: 0;"> <span id="LC3267" class="line" lang="cpp"> <span class="n" style="color: #333;">startVerbose</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// talkative during initialization</span></span>
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3268
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3268
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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span> <span class="cm" style="color: #998; font-style: italic;">/*passMemExc*/</span><span class="p">,</span></span>
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3269
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<pre style="margin: 0;">-<span id="LC3269" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">);</span></span>
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3269
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<pre style="margin: 0;">+<span id="LC3269" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">,</span></span>
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3270
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<pre style="margin: 0;">+<span id="LC3270" class="line" lang="cpp"> <span class="n" style="color: #333;">isBt2Index</span><span class="p">);</span></span>
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3271
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<pre style="margin: 0;"> <span id="LC3271" class="line" lang="cpp"> <span class="n" style="color: #333;">Ebwt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">ebwtBw</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3271
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3272
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<pre style="margin: 0;"> <span id="LC3272" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We need the mirror index if mismatches are allowed</span></span>
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3272
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3273
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<pre style="margin: 0;"> <span id="LC3273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">maqLike</span><span class="p">)</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">@@ -3287,7 +3288,8 @@ static void driver(const char * type,</td>
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3287
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3288
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<pre style="margin: 0;"> <span id="LC3288" class="line" lang="cpp"> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// whether to be talkative</span></span>
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3288
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3289
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<pre style="margin: 0;"> <span id="LC3289" class="line" lang="cpp"> <span class="n" style="color: #333;">startVerbose</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// talkative during initialization</span></span>
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3289
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3290
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<pre style="margin: 0;"> <span id="LC3290" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span> <span class="cm" style="color: #998; font-style: italic;">/*passMemExc*/</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC3290" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">);</span></span>
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3291
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<pre style="margin: 0;">+<span id="LC3291" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheck</span><span class="p">,</span></span>
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3292
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<pre style="margin: 0;">+<span id="LC3292" class="line" lang="cpp"> <span class="n" style="color: #333;">isBt2Index</span><span class="p">);</span></span>
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3293
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<pre style="margin: 0;"> <span id="LC3293" class="line" lang="cpp"> <span class="p">}</span></span>
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3294
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<pre style="margin: 0;"> <span id="LC3294" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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3295
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<pre style="margin: 0;"> <span id="LC3295" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#78173a2355322cb62fac5714cd9aa8361ca724e7"><strong>filebuf.h</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">@@ -13,6 +13,8 @@</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <fcntl.h></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "assert_helpers.h"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -49,6 +51,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">FileBuf</span><span class="p">(</span><span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="p">{</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">_zIn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_zIn</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="p">}</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">FileBuf</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;">ifstream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inf</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">init</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inf</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">@@ -65,7 +73,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Return true iff there is a stream ready to read.</span></span>
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66
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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67
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isOpen</span><span class="p">()</span> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_<span class="idiff left">zIn</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">NULL</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 right">_</span>inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="p">}</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="84" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -76,7 +84,9 @@ public:</td>
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76
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">_in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <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;">_inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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78
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">_inf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <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;">_zIn</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">_zIn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// can't close _ins</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="p">}</span></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <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">@@ -85,7 +95,7 @@ public:</td>
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85
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Get the next character of input and advance.</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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87
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">get</span><span class="p">()</span> <span class="p">{</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_<span class="idiff left">zIn</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">NULL</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 right">_</span>inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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89
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">peek</span><span class="p">();</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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91
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">_cur</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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,6 +123,19 @@ public:</td>
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113
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">_done</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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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="p">}</span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Initialize the buffer with a new gz file.</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">newFile</span><span class="p">(</span><span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="p">{</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">_zIn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">_buf_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">_done</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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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="p">}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"></span>
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116
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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117
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Initialize the buffer with a new ifstream.</span></span>
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118
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="171" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -148,6 +171,8 @@ public:</td>
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148
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <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;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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149
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<td class="diff-line-num new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">_ins</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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150
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">_ins</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seekg</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;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">beg</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <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;">_zIn</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">gzrewind</span><span class="p">(</span><span class="n" style="color: #333;">_zIn</span><span class="p">);</span></span>
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151
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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152
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">rewind</span><span class="p">(</span><span class="n" style="color: #333;">_in</span><span class="p">);</span></span>
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153
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -162,7 +187,7 @@ public:</td>
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162
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Occasionally we'll need to read in a new buffer's worth of data.</span></span>
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163
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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164
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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">peek</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_<span class="idiff left">zIn</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">NULL</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 right">_</span>inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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166
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">_cur</span><span class="p">,</span> <span class="n" style="color: #333;">_buf_sz</span><span class="p">);</span></span>
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167
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_cur</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_buf_sz</span><span class="p">)</span> <span class="p">{</span></span>
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168
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_done</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="175" style="width: 35px; color: rgba(0,0,0,0.3); 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="200" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -175,6 +200,8 @@ public:</td>
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175
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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176
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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">_inf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</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="p">)</span><span class="n" style="color: #333;">_buf</span><span class="p">,</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">);</span></span>
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177
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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">_buf_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_inf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gcount</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <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;">_zIn</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">_buf_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzread</span><span class="p">(</span><span class="n" style="color: #333;">_zIn</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_buf</span><span class="p">,</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">);</span></span>
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178
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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> <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;">_ins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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179
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="n" style="color: #333;">_ins</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</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="p">)</span><span class="n" style="color: #333;">_buf</span><span class="p">,</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">);</span></span>
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180
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<td class="diff-line-num new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">_buf_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ins</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gcount</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">@@ -333,10 +360,44 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_lastn_cur</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c"> <span class="p">}</span></span>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="c"></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isGzippedFile</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;">filename</span><span class="p">)</span> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="c"> <span class="p">}</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="c"></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">O_RDONLY</span><span class="p">);</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="c"> <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;">"Unable to open "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="c"> <span class="n" style="color: #333;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="c"> <span class="p">}</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="c"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">byte1</span><span class="p">,</span> <span class="n" style="color: #333;">byte2</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="c"></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">ssize_t</span> <span class="n" style="color: #333;">r1</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;">fd</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">byte1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">ssize_t</span> <span class="n" style="color: #333;">r2</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;">fd</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">byte2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">));</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="c"> <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;">close</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="c"> <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;">"Unable to close "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="c"> <span class="n" style="color: #333;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c"> <span class="p">}</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" 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="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="c"> <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;">"Unable to read file magic number"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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="c"></span>
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<td class="diff-line-num new new_line" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">byte1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x1f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">byte2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x8b</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="c"> <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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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="c"> <span class="p">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="c"></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="c"> <span class="p">}</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="c"></span>
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336
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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337
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"></span>
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338
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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">init</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="diff-line-num 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">
339
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<td class="diff-line-num new_line" 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="c"> <span class="n" style="color: #333;">_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c"> <span class="n" style="color: #333;">_zIn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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340
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<td class="diff-line-num new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="n" style="color: #333;">_inf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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="c"> <span class="n" style="color: #333;">_ins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" 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">
342
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<td class="diff-line-num new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">_cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_buf_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUF_SZ</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -347,6 +408,7 @@ private:</td>
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347
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="c"></span>
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348
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">BUF_SZ</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">256</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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349
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_in</span><span class="p">;</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">_zIn</span><span class="p">;</span></span>
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350
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_inf</span><span class="p">;</span></span>
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351
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_ins</span><span class="p">;</span></span>
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352
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">_cur</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#f06297a2ada54367ed9d9c768f848c4726441af2"><strong>hit.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -169,7 +169,6 @@ public:</td>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">nthreads_</span><span class="p">((</span><span class="n" style="color: #333;">nthreads</span> <span class="o" style="font-weight: 600;">></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;">nthreads</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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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">ptBufs_</span><span class="p">(),</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">ptCounts_</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">),</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">batchIds_</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">),</span></span>
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173
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">perThreadBufSize_</span><span class="p">(</span><span class="n" style="color: #333;">perThreadBufSize</span><span class="p">),</span></span>
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174
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">ptNumAligned_</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span></span>
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175
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">reorder_</span><span class="p">(</span><span class="n" style="color: #333;">reorder</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,8 +182,6 @@ public:</td>
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183
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">ptNumMaxed_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptNumUnaligned_</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nthreads_</span><span class="p">;</span></span>
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184
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="n" style="color: #333;">ptBufs_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">);</span></span>
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185
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">ptCounts_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">batchIds_</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">lastBatchIdSeen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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188
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">initDumps</span><span class="p">();</span></span>
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189
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="p">}</span></span>
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190
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -253,9 +250,6 @@ public:</td>
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253
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="p">}</span></span>
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254
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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255
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">ptCounts_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reorder_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">batchIds_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rdid</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">perThreadBufSize_</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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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="p">}</span></span>
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259
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tally</span><span class="p">)</span> <span class="p">{</span></span>
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260
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">tallyAlignments</span><span class="p">(</span><span class="n" style="color: #333;">threadId</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;">start</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">);</span></span>
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261
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,10 +262,10 @@ public:</td>
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268
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hadoopOut</span><span class="p">)</span> <span class="p">{</span></span>
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269
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Flush all per-thread buffers</span></span>
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270
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">flushAll</span><span class="p">();</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c"><span class="idiff left right"> </span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c"></span>
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272
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Close all output streams</span></span>
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273
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">closeOuts</span><span class="p">();</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c"><span class="idiff left right"> </span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"></span>
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275
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Print information about how many unpaired and/or paired</span></span>
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276
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// reads were aligned.</span></span>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"> <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;">quiet_</span><span class="p">)</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">@@ -285,7 +279,7 @@ public:</td>
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="n" style="color: #333;">numUnaligned</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ptNumUnaligned_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">numMaxed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ptNumMaxed_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="c"></span>
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289
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numUnaligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numMaxed</span><span class="p">;</span></span>
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290
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alPct</span> <span class="o" style="font-weight: 600;">=</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;">unalPct</span> <span class="o" style="font-weight: 600;">=</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;">maxPct</span> <span class="o" style="font-weight: 600;">=</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>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -560,44 +554,21 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Flush thread's output buffer and reset both buffer and count.</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">flush</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">f<span class="idiff left right">inalBatch</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">flush</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">f<span class="idiff left right">orce</span></span><span class="p">)</span> <span class="p">{</span></span>
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564
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"> <span class="p">{</span></span>
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565
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">_ts</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex_</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// flush</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reorder_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="c"> <span class="n" style="color: #333;">nchars</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ptBufs_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</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="LC568" class="line" lang="c"> <span class="n" style="color: #333;">batch</span> <span class="n" style="color: #333;">b</span><span class="p">(</span><span class="n" style="color: #333;">ptBufs_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">],</span> <span class="n" style="color: #333;">batchIds_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span> <span class="cm" style="color: #998; font-style: italic;">/* has batch been written */</span><span class="p">);</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="c"> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// consider writing if we have enough data to fill the buffer</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// or we're ready to output the final batch</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">finalBatch</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">nchars</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">OutFileBuf</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BUF_SZ</span><span class="p">)</span> <span class="p">{</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// sort by batch ID</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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;">batch</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">size_type</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;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">size</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 class="p">{</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">batchId</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lastBatchIdSeen</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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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="c"> <span class="n" style="color: #333;">nchars</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">out_</span><span class="p">.</span><span class="n" style="color: #333;">writeString</span><span class="p">(</span><span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">btString</span><span class="p">);</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="c"> <span class="n" style="color: #333;">lastBatchIdSeen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">batchId</span><span class="p">;</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">isWritten</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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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="c"> <span class="p">}</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="c"> <span class="p">}</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="c"> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">erase</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;">remove_if</span><span class="p">(</span><span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="c"> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">batch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove_written_batches</span><span class="p">),</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="c"> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="c"> <span class="p">}</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="c"> <span class="p">}</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="c"> <span class="n" style="color: #333;">out_</span><span class="p">.</span><span class="n" style="color: #333;">writeString</span><span class="p">(</span><span class="n" style="color: #333;">ptBufs_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]);</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="c"> <span class="p">}</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="c"> <span class="n" style="color: #333;">out_</span><span class="p">.</span><span class="n" style="color: #333;">writeString</span><span class="p">(</span><span class="n" style="color: #333;">ptBufs_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]);</span></span>
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590
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c"> <span class="p">}</span></span>
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591
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="c"> <span class="n" style="color: #333;">ptCounts_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</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>
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592
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="c"> <span class="n" style="color: #333;">ptBufs_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">].</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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593
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="c"> <span class="p">}</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="c"><span class="idiff left right"> </span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"></span>
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595
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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596
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Flush all output buffers.</span></span>
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597
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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598
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">flushAll</span><span class="p">()</span> <span class="p">{</span></span>
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599
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c"> <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;">nthreads_</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 class="p">{</span></span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">flush</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">i</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">nthreads_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="c"> <span class="n" style="color: #333;">flush</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">true</span></span><span class="p">);</span></span>
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601
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="c"> <span class="p">}</span></span>
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602
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="c"> <span class="p">}</span></span>
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603
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); 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="581" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -610,7 +581,7 @@ protected:</td>
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610
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">flush</span><span class="p">(</span><span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span> <span class="cm" style="color: #998; font-style: italic;">/* final batch? */</span><span class="p">);</span></span>
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611
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"> <span class="p">}</span></span>
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612
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="p">}</span></span>
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613
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Close (and flush) all OutFileBufs.</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</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">@@ -621,49 +592,14 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="c"> <span class="n" style="color: #333;">OutFileBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// the alignment output stream(s)</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">vector</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;">_refnames</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// map from reference indexes to names</span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="c"> <span class="n" style="color: #333;">MUTEX_T</span> <span class="n" style="color: #333;">mutex_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// pthreads mutexes for per-file critical sections</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// used for output read buffer<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// used for output read buffer</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nthreads_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c"> <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;">BTString</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ptBufs_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="c"> <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;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ptCounts_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">perThreadBufSize_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">reorder_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">batch</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="c"> <span class="n" style="color: #333;">BTString</span> <span class="n" style="color: #333;">btString</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">batchId</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isWritten</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="c"> <span class="n" style="color: #333;">batch</span><span class="p">(</span><span class="n" style="color: #333;">BTString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">batchId</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">),</span> <span class="n" style="color: #333;">isWritten</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">moveTo</span><span class="p">(</span><span class="n" style="color: #333;">btString</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">batch</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">other</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">batchId</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;">batchId</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="c"> <span class="n" style="color: #333;">batch</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">batch</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="LC648" class="line" lang="c"> <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;">other</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">this</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="c"> <span class="n" style="color: #333;">batchId</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;">batchId</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="c"> <span class="n" style="color: #333;">isWritten</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;">isWritten</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="c"> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">btString</span><span class="p">.</span><span class="n" style="color: #333;">moveTo</span><span class="p">(</span><span class="n" style="color: #333;">btString</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">remove_written_batches</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">batch</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">isWritten</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="c"> <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;">batch</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">unwrittenBatches_</span><span class="p">;</span></span>
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663
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="c"> <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;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">batchIds_</span><span class="p">;</span></span>
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664
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">lastBatchIdSeen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nchars</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="c"></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Output filenames for dumping</span></span>
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <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;">dumpAlBase_</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <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;">dumpUnalBase_</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1100,7 +1036,7 @@ public:</td>
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1100
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">HitSinkPerThread</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">create</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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1101
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">NGoodHitSinkPerThread</span><span class="p">(</span><span class="n" style="color: #333;">sink_</span><span class="p">,</span> <span class="n" style="color: #333;">n_</span><span class="p">,</span> <span class="n" style="color: #333;">max_</span><span class="p">,</span> <span class="n" style="color: #333;">defaultMapq_</span><span class="p">,</span> <span class="n" style="color: #333;">threadId_</span><span class="p">);</span></span>
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1102
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="c"> <span class="p">}</span></span>
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1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="c"><span class="idiff left right"> </span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="c"></span>
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1104
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1040
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">HitSinkPerThread</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">createMult</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">m</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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1105
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">max_</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0xffffffff</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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1106
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</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="mh" style="color: #099;">0xffffffff</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1243,7 +1179,7 @@ public:</td>
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1243
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">HitSinkPerThread</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">create</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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1244
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">NBestFirstStratHitSinkPerThread</span><span class="p">(</span><span class="n" style="color: #333;">sink_</span><span class="p">,</span> <span class="n" style="color: #333;">n_</span><span class="p">,</span> <span class="n" style="color: #333;">max_</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">defaultMapq_</span><span class="p">,</span> <span class="n" style="color: #333;">threadId_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1246" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">HitSinkPerThread</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">createMult</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">m</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">max_</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0xffffffff</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</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="mh" style="color: #099;">0xffffffff</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#7c4ae52e4a13c990d16c9530fb874ed79064a5cd"><strong>pat.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">@@ -765,6 +765,7 @@ pair<bool, int> FastaContinuousPatternSource::nextBatchFromFile(</td>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// can re-use this prefix for all the reads</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that are substrings of this FASTA sequence</span></span>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">name_prefix_buf_</span><span class="p">[</span><span class="n" style="color: #333;">nameoff</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;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">subReadCnt_</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getc_wrapper</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC771" 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">@@ -794,13 +795,14 @@ pair<bool, int> FastaContinuousPatternSource::nextBatchFromFile(</td>
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the sampling gaps are by looking at the read</span></span>
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// name</span></span>
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<pre style="margin: 0;"> <span id="LC797" 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;">beginning_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">r</span>eadCnt_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">subR</span>eadCnt_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"> <span class="p">}</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="cpp"> <span class="p">}</span></span>
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// install name</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">nameoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">name_prefix_buf_</span><span class="p">);</span></span>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">,</span> <span class="n" style="color: #333;">name_prefix_buf_</span><span class="p">,</span> <span class="n" style="color: #333;">nameoff</span><span class="p">);</span></span>
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803
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TReadId</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">readCnt_</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">subReadCnt_</span><span class="p">,</span> <span class="n" style="color: #333;">name_int_buf_</span><span class="p">);</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TReadId</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">subReadCnt_</span><span class="p">,</span> <span class="n" style="color: #333;">name_int_buf_</span><span class="p">);</span></span>
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804
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bufoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nameoff</span><span class="p">;</span></span>
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805
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufoff</span><span class="p">,</span> <span class="n" style="color: #333;">name_int_buf_</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">name_int_buf_</span><span class="p">));</span></span>
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806
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"> <span class="n" style="color: #333;">bufoff</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">name_int_buf_</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); 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="819" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -817,8 +819,8 @@ pair<bool, int> FastaContinuousPatternSource::nextBatchFromFile(</td>
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817
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp"> <span class="p">}</span></span>
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818
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBufLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bufoff</span><span class="p">;</span></span>
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819
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"> <span class="n" style="color: #333;">eat_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">freq_</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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820
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">readCnt_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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821
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">beginning_</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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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"> <span class="n" style="color: #333;">subReadCnt_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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822
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">readi</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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823
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"> <span class="p">}</span></span>
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824
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826
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<pre style="margin: 0;"> <span id="LC826" 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="861" style="width: 35px; color: rgba(0,0,0,0.3); 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="863" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -861,9 +863,9 @@ bool FastaContinuousPatternSource::parse(</td>
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861
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="cpp"></span>
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862
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse sequence</span></span>
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863
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">seqan</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">length</span><span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">));</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">[</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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865
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nchar</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;">seqoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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866
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">buflen</span><span class="p">)</span> <span class="p">{</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">[</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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867
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isalpha</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">))</span> <span class="p">{</span></span>
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868
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_in</span><span class="p">(</span><span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">),</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">);</span></span>
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869
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nchar</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">>=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trim5_</span><span class="p">)</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">@@ -871,7 +873,6 @@ bool FastaContinuousPatternSource::parse(</td>
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871
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patBufFw</span><span class="p">[</span><span class="n" style="color: #333;">seqoff</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;">charToDna5</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// ascii to int</span></span>
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872
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp"> <span class="p">}</span></span>
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="cpp"> <span class="p">}</span></span>
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874
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">[</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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875
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="cpp"> <span class="p">}</span></span>
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876
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patBufFw</span><span class="p">[</span><span class="n" style="color: #333;">seqoff</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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877
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"> <span class="n" style="color: #333;">_setBegin</span><span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">Dna5</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patBufFw</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); 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="1330" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1329,14 +1330,18 @@ pair<bool, int> RawPatternSource::nextBatchFromFile(</td>
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1329
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1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read until we run out of input or until we've filled the buffer</span></span>
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1330
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1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="n" style="color: #333;">readi</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;">max_buf_</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c</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;">readi</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1331
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBufLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1333" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">[</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBufLen</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;">c</span><span class="p">;</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">))</span> <span class="p">{</span></span>
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1334
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getc_wrapper</span><span class="p">();</span></span>
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1335
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1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">))</span> <span class="p">{</span></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\r'</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">[</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBufLen</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;">c</span><span class="p">;</span></span>
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getc_wrapper</span><span class="p">();</span></span>
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1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="cpp"> <span class="p">}</span></span>
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"> <span class="p">}</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</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;">readOrigBufLen</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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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">readi</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="cpp"> <span class="p">}</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="cpp"></span>
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">c</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;">readi</span><span class="p">);</span></span>
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="cpp"><span class="p">}</span></span>
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#feeebf6c8e249c25303af46ea1abd54e5f54b5db"><strong>processor_support.h</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Utility class ProcessorSupport provides POPCNTenabled() to determine</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// processor support for POPCNT instruction. It uses CPUID to</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// retrieve the processor capabilities.</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for Intel ICC compiler __cpuid() is an intrinsic<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for Intel ICC compiler __cpuid() is an intrinsic</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for Microsoft compiler __cpuid() is provided by #include <intrin.h></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// for GCC compiler __get_cpuid() is provided by #include <cpuid.h></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"></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">@@ -25,10 +25,10 @@ struct regs_t {unsigned int EAX, EBX, ECX, EDX;};</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">ProcessorSupport</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef POPCNT_CAPABILITY<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef POPCNT_CAPABILITY</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">ProcessorSupport</span><span class="p">()</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="LC30" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">ProcessorSupport</span><span class="p">()</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">POPCNTenabled</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// from: Intel® 64 and IA-32 Architectures Software Developer’s Manual, 325462-036US,March 2013</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">@@ -44,12 +44,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if ( defined(USING_INTEL_COMPILER) || defined(USING_MSC_COMPILER) )</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">__cpuid</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></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;">regs</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// test if __cpuid() works, if not catch the exception</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">__cpuid</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></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;">regs</span><span class="p">,</span><span class="mh" style="color: #099;">0x1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// POPCNT bit is bit 23 in ECX</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">__cpuid</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></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;">regs</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// test if __cpuid() works, if not catch the exception</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">__cpuid</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></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;">regs</span><span class="p">,</span><span class="mh" style="color: #099;">0x1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// POPCNT bit is bit 23 in ECX</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif defined(USING_GCC_COMPILER)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">__get_cpuid</span><span class="p">(</span><span class="mh" style="color: #099;">0x1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">EAX</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">EBX</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">ECX</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">EDX</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <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="err" style="color: #a61717; background-color: #e3d2d2;">“</span><span class="n" style="color: #333;">ERROR</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">__cpuid</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">build</span><span class="p">.</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="n" style="color: #333;">n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">”</span><span class="p">;</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <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="err" style="color: #a61717; background-color: #e3d2d2;">“</span><span class="n" style="color: #333;">ERROR</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">define</span> <span class="n" style="color: #333;">__cpuid</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">build</span><span class="p">.</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="n" style="color: #333;">n</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">”</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">assert</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="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">ECX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BIT</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">regs</span><span class="p">.</span><span class="n" style="color: #333;">ECX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BIT</span><span class="p">(</span><span class="mi" style="color: #099;">23</span><span class="p">))</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>
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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">@@ -64,7 +64,3 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/*PROCESSOR_SUPPORT_H_*/</span></span></pre>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#8cb73317275ca3f68e13f1344310abe501fa6653"><strong>sam.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">@@ -139,9 +139,6 @@ void SAMHitSink::reportUnOrMax(</td>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\n'</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 class="n" style="color: #333;">ptCounts_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reorder_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">batchIds_</span><span class="p">[</span><span class="n" style="color: #333;">threadId</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">perThreadBufSize_</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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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC144" 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 old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -337,7 +334,7 @@ void SAMHitSink::reportMaxed(</td>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strat</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;">hs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">stratum</span><span class="p">,</span> <span class="n" style="color: #333;">hs</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="n" style="color: #333;">stratum</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bestStratum</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">reportHits</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hs</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">hs</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;">2</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="nb" style="color: #0086b3;"><span class="idiff left right">fals</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">reportHits</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hs</span><span class="p">,</span> <span class="n" style="color: #333;">i</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;">2</span><span class="p">,</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">hs</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;">2</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="nb" style="color: #0086b3;"><span class="idiff left right">tru</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC338" 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="LC339" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">num</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,7 +349,7 @@ void SAMHitSink::reportMaxed(</td>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">num</span><span class="p">,</span> <span class="n" style="color: #333;">hs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rand</span><span class="p">.</span><span class="n" style="color: #333;">nextU32</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">reportHits</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hs</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">hs</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="nb" style="color: #0086b3;"><span class="idiff left right">fals</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">reportHits</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hs</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">threadId</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">hs</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="nb" style="color: #0086b3;"><span class="idiff left right">tru</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC354" 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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358
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">reportUnOrMax</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hs</span><span class="p">,</span> <span class="n" style="color: #333;">threadId</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="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">while </span><span class="nb" style="color: #0086b3;">getopts</span> <span class="s2" style="color: #d14;">"sb:"</span> opt<span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: #008080;">$opt</span> <span class="k" style="font-weight: 600;">in</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>s<span class="p">)</span> <span class="nv" style="color: #008080;">use_sra</span><span class="o" style="font-weight: 600;">=</span>1 <span class="p">;;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> b<span class="p">)</span> <span class="nv" style="color: #008080;">branch</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$OPTARG</span><span class="s2" style="color: #d14;">"</span> <span class="p">;;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Usage: </span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;"> [-s] [-b <branch_name>]"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">shift</span> <span class="k" style="font-weight: 600;">$((</span><span class="nv" style="color: #008080;">$OPTIND</span> <span class="o" style="font-weight: 600;">-</span> <span class="m" style="color: #099;">1</span><span class="k" style="font-weight: 600;">))</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$branch</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">branch</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"master"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">yum <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> git zip unzip pandoc</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">git clone https://github.com/BenLangmead/bowtie.git</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to clone bowtie repo"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>bowtie</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">pwd</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">ls</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">git branch <span class="nt" style="color: #000080;">-a</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$branch</span><span class="s2" style="color: #d14;">"</span> 2>&1 <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"branch '</span><span class="nv" style="color: #008080;">$branch</span><span class="s2" style="color: #d14;">' does not exist"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>git checkout <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$branch</span><span class="s2" style="color: #d14;">"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$use_sra</span> <span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># this variant is needed to compile ncbi-vdb</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">source</span> /hbb/activate</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> make sra-deps</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this variant creates static binaries with PIC</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source</span> /hbb_exe_gc_hardened/activate</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> /mybin</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'res=`echo $@ | sed "s/-L.*$//"`; echo $res; echo $res; /opt/rh/devtoolset-7/root/usr/bin/ar $res;'</span> <span class="o" style="font-weight: 600;">></span> /mybin/ar</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> +x /mybin/ar <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/mybin:<span class="nv" style="color: #008080;">$PATH</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># make static-libs</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ $? -ne 0 ] ; then</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Unable to build tbb and/or zlib static dependencies"</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># exit 1</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">make bowtie-bin.zip <span class="nv" style="color: #008080;">RELEASE_BUILD</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">EXTRA_FLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--std=c++98"</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to create bowtie package"</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running libcheck..."</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell">libcheck bowtie-<span class="o" style="font-weight: 600;">{</span>align,build,inspect<span class="o" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">*</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running hardening check..."</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell">hardening-check <span class="nt" style="color: #000080;">-b</span> bowtie-<span class="o" style="font-weight: 600;">{</span>align,build,inspect<span class="o" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">*</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Copying binary package"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /bowtie/<span class="k" style="font-weight: 600;">*</span>.zip /io</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#3dc9a13f2402854ca8fc5e4a0ced7b5d0012b83c"><strong>scripts/run-hbb.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">bowtie_root</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PWD</span><span class="p">%%bowtie*</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/bowtie"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">docker run <span class="nt" style="color: #000080;">-t</span> <span class="nt" style="color: #000080;">-i</span> <span class="nt" style="color: #000080;">--rm</span> <span class="se" style="color: #d14;">\</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$bowtie_root</span>:/io <span class="se" style="color: #d14;">\</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> phusion/holy-build-box-64:latest <span class="se" style="color: #d14;">\</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> bash /io/scripts/bowtie-hbb.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/commit/8fdd41caa10ed179fa67b07803e754b6faca52a5#1ba32b1a76b5b57a56e4d834114b45c9fbeb218e"><strong>shmem.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,7 +67,7 @@ bool allocSharedMem(std::string fname,</td>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"EEXIST"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <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;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EINVAL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
69
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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: shared-memory chunk's segment size doesn't match expected size ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">shmemLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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70
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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Delet<span class="idiff left right">e</span>ing old shared memory block and trying again."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Deleting old shared memory block and trying again."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">shmid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shmget</span><span class="p">(</span><span class="n" style="color: #333;">key</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>
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<td class="diff-line-num 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">
72
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<td class="diff-line-num new_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">
72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shmctl</span><span class="p">(</span><span class="n" style="color: #333;">shmid</span><span class="p">,</span> <span class="n" style="color: #333;">IPC_RMID</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ds</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="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"shmctl returned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ret</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); 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="105" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -105,7 +105,7 @@ bool allocSharedMem(std::string fname,</td>
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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">shm_segsz</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">shmemLen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: shared-memory chunk's segment size ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">shm_segsz</span></span>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") doesn't match expected size ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shmemLen</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Delet<span class="idiff left right">e</span>ing old shared memory block and trying again."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" 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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<td class="diff-line-num new new_line" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Deleting old shared memory block and trying again."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shmctl</span><span class="p">(</span><span class="n" style="color: #333;">shmid</span><span class="p">,</span> <span class="n" style="color: #333;">IPC_RMID</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ds</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="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"shmctl returned "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for IPC_RMID and errno is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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