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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/a87dec4f5896357452377c8df6169de6609b2822">a87dec4f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-05-29T19:11:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1296</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/843775686df5452428a91b18d60386a7232ef761">84377568</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-05-29T19:12:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1296'
Update to upstream version '1296'
with Debian dir 5ad1f4db1f2c22ccc01dc76e8a9ba62239a9a5d2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/71f98fd6f1fa5620a9ab40e2628f954ec44d89ee">71f98fd6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-05-29T19:12:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.6.1 (no changes needed)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/ad07ecda317748675675d73e4a32901e9f0413b3">ad07ecda</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-05-29T19:13:07+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#970fc983e9aedfff96d9edf69624a5023e7fcba4">
bin/maf-cut
</a>
</li>
<li class="file-stats">
<a href="#37ed2ad62deb0a258c42561b3b9c51e734cc517e">
bin/parallel-fasta
</a>
</li>
<li class="file-stats">
<a href="#b6cf74e7adde22c20c057b966204093b4d4a5aa7">
bin/parallel-fastq
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</li>
<li class="file-stats">
<a href="#062baa88bb03951a036716bb1775a09eade2439e">
build/seed-doc.sh
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</li>
<li class="file-stats">
<a href="#c08354c0b0830a059880a852680dec5f7003bfb8">
data/RY16-8.seed
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<li class="file-stats">
<a href="#f2751d8625d2277c99120885eaad1a35aceef91d">
data/RY32-10.seed
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<li class="file-stats">
<a href="#d4865a426f82cbe8dc69174553ff32a71d5fc7b8">
data/RY4-6.seed
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<li class="file-stats">
<a href="#ff2c3344642495a5d57dfe6c736ac9785228e4f9">
data/RY8-8.seed
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#6da0343fd1e96c9faaa35ff4e058c0bb04191144">
doc/last-cookbook.rst
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<li class="file-stats">
<a href="#1bbcf798dd6c7dc9ad18596c421c40c0196ed866">
doc/last-map-probs.rst
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</li>
<li class="file-stats">
<a href="#ddeca73099d2ddf58518033faefe70ad37b8745d">
doc/last-parallel.rst
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<li class="file-stats">
<a href="#977fadb853a729d73f897f1532ab693a2edb5af2">
doc/last-seeds.rst
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<li class="file-stats">
<a href="#3df0be4654dc98e9c961572d8d1876b21024c1d2">
doc/maf-cut.rst
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<li class="file-stats">
<a href="#d0552713235c86a577163a3f58b56207610ad394">
src/CyclicSubsetSeed.cc
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</li>
<li class="file-stats">
<a href="#38e88d72aa956d3886597351d58b37469947a653">
src/CyclicSubsetSeed.hh
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<li class="file-stats">
<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">
src/LastalArguments.cc
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<li class="file-stats">
<a href="#b8ecac13f5a049cde8c83663390da1d0fc2bd9a1">
src/fileMap.cc
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<li class="file-stats">
<a href="#de4252990d12a909e50ff0b994d1715eae0ea5fd">
src/lastdb.cc
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<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
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<li class="file-stats">
<a href="#6c90adec85ff9834658c43a287e5d780f52732ef">
test/last-test.out
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<li class="file-stats">
<a href="#fcd3167fe23623673ee838f0da31855d3d479dff">
test/last-test.sh
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<li class="file-stats">
<a href="#a279e6bc3648ec4fa6cb7f05adccc78e0c01ad8a">
<span class="new-file">
+
test/maf-cut-test.out
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</li>
<li class="file-stats">
<a href="#5f1ef9aa98b3328c3327e88496805261dd201ca8">
<span class="new-file">
+
test/maf-cut-test.sh
</span>
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</li>
</ul>
<h4>Changes:</h4>
<li id="970fc983e9aedfff96d9edf69624a5023e7fcba4">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#970fc983e9aedfff96d9edf69624a5023e7fcba4"><strong>bin/maf-cut</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,9 +3,10 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(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="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<td class="old_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">optparse</span></span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">signal</span></span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,13 +57,28 @@ def findTheSpecifiedSequence(seqName, mafLines):</td>
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<td class="old_line diff-line-num" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
56
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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fields</span></span>
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<td class="old_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
57
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<td class="new_line diff-line-num" 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">
58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="old_line diff-line-num" 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">
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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">addMafData</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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;">"s"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</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;"># xxx omit theSpecifiedSequence ?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">oldSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</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;">alnBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alnEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" 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">
71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">beg</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;">seqLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">beg</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">seqData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqLen</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span></span>
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73
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqData</span><span class="p">)</span></span>
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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59
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75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cutMafRecords</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">):</span></span>
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60
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76
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span></span>
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61
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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62
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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;">"s"</span><span class="p">:</span></span>
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63
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79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">oldSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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64
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80
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">newSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">[</span><span class="n" style="color: #333;">alnBeg</span><span class="p">:</span><span class="n" style="color: #333;">alnEnd</span><span class="p">]</span></span>
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65
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</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;">alnBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">oldSeq</span><span class="p"><span class="idiff left deletion">[:</span></span><span class="n" style="color: #333;"><span class="idiff deletion">alnBeg</span></span><span class="p"><span class="idiff right deletion">]</span>.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</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;">alnBeg</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">oldSeq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">alnBeg</span></span><span class="p">)</span></span>
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66
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82
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">newSeq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newSeq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>
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67
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83
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">fields</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">span</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">newSeq</span><span class="p">]</span></span>
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68
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84
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</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;">"q"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); 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="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,15 +98,7 @@ def printMafLine(fieldWidths, fields):</td>
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82
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98
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">formatParams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">from_iterable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">fieldWidths</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">))</span></span>
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83
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99
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%*s %-*s %*s %*s %*s %*s %*s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">formatParams</span><span class="p">))</span></span>
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84
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100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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85
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>
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86
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutRange</span></span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">sLineFields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findTheSpecifiedSequence</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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88
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" 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;">sLineFields</span><span class="p">:</span></span>
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89
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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90
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentRange</span><span class="p">(</span><span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">)</span></span>
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91
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">:</span></span>
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92
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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93
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">mafRecords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cutMafRecords</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafRecords</span><span class="p">):</span></span>
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102
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">fieldWidths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">mafFieldWidths</span><span class="p">(</span><span class="n" style="color: #333;">mafRecords</span><span class="p">))</span></span>
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103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fields</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafRecords</span><span class="p">:</span></span>
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104
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</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;">"s"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,15 +111,75 @@ def cutOneMaf(cutRange, mafLines):</td>
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103
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">))</span></span>
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104
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>
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105
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113
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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106
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<td class="new_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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107
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<td class="new_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nameFromTitleLine</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:].</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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116
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doOneFastaSequence</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">seqLines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">alnData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">nameFromTitleLine</span><span class="p">(</span><span class="n" style="color: #333;">topLine</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnData</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqLines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">alnData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</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;">seqLen</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnData</span><span class="p">:</span></span>
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124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span><span class="p">)</span></span>
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">beg</span><span class="p">:</span><span class="n" style="color: #333;">end</span><span class="p">])</span></span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doOneFastqSequence</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">alnData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">nameFromTitleLine</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnData</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">seqLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">alnData</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</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;">seqLen</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnData</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alnData</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">beg</span><span class="p">:</span><span class="n" style="color: #333;">end</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="n" style="color: #333;">beg</span><span class="p">:</span><span class="n" style="color: #333;">end</span><span class="p">])</span></span>
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141
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printFastaParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">seqLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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108
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144
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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109
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">isspace</span><span class="p">():</span></span>
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110
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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111
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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112
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</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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113
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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114
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">doOneFastaSequence</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">seqLines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">topLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">seqLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">seqLines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">doOneFastaSequence</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">seqLines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printFastqParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">topLine</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">topLine</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</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;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">doOneFastqSequence</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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160
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161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printSequenceParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">printFastaParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</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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<td class="new_line diff-line-num new" 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">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">printFastqParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">lines</span><span class="p">)</span></span>
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167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"can't read the sequence data"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">sLineFields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findTheSpecifiedSequence</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" 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;">sLineFields</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentRange</span><span class="p">(</span><span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">sLineFields</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alnBeg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" 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">
178
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dataPerSeq</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">mafRecords</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cutMafRecords</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">printOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafRecords</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">addMafData</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">alnBeg</span><span class="p">,</span> <span class="n" style="color: #333;">alnEnd</span><span class="p">)</span></span>
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183
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="python"></span>
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184
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wantedRange</span><span class="p">(</span><span class="n" style="color: #333;">cutSpecification</span><span class="p">):</span></span>
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185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -120,20 +188,32 @@ def wantedRange(cutSpecification):</td>
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120
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188
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">beg</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;">cutSpecification</span><span class="p">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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121
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189
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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122
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190
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></span>
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123
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC123" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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124
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">cutRange</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wantedRange</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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125
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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126
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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127
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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128
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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129
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<td class="new_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">mafCutOneFile</span><span class="p">(</span><span class="n" style="color: #333;">cutRange</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">)</span></span>
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191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wantedRange</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">segment</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">dataPerSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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194
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">alignments</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">isspace</span><span class="p">():</span></span>
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198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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199
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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200
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</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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201
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">mafLines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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202
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">cutOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">cutBeg</span><span class="p">,</span> <span class="n" style="color: #333;">cutEnd</span><span class="p">,</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>
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203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dataPerSeq</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fileName</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">:</span></span>
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206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">printSequenceParts</span><span class="p">(</span><span class="n" style="color: #333;">dataPerSeq</span><span class="p">,</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">))</span></span>
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130
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207
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>
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131
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208
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" 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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132
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209
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">signal</span><span class="p">(</span><span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIGPIPE</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">.</span><span class="n" style="color: #333;">SIG_DFL</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># avoid silly error message</span></span>
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133
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<td class="new_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">usage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%prog chrN:start-end alignments.maf"</span></span>
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134
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<td class="new_line diff-line-num" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
210
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Get parts of MAF-format alignments."</span></span>
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135
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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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136
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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">opts</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;">op</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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137
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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC137" 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;">args</span><span class="p">:</span></span>
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138
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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"please give me a cut specification and MAF alignments"</span><span class="p">)</span></span>
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139
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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span></pre></td>
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211
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">ap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">ap</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"segment"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"zero-based sequence range, e.g. chr7:123400-123500"</span><span class="p">)</span></span>
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214
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">ap</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"alignments"</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"?"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file of sequence alignments in MAF format"</span><span class="p">)</span></span>
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216
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">ap</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"sequences"</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"*"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># xxx need default?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file of sequences in fasta or fastq format"</span><span class="p">)</span></span>
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218
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ap</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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219
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">mafCut</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#37ed2ad62deb0a258c42561b3b9c51e734cc517e"><strong>bin/parallel-fasta</strong></a>
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/sh</span></span>
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2
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--version</span> <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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4
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5
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--minversion</span> 20130222 <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">||</span></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span>: warning: old version of parallel, might be slow 1>&2</span>
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7
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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8
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--pipe</span> <span class="nt" style="color: #000080;">--recstart</span> <span class="s1" style="color: #d14;">'>'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre></td>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>parallel <span class="nt" style="color: #000080;">--round</span> <span class="nt" style="color: #000080;">--recstart</span> <span class="s1" style="color: #d14;">'>'</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#b6cf74e7adde22c20c057b966204093b4d4a5aa7"><strong>bin/parallel-fastq</strong></a>
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1
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/sh</span></span>
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2
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--version</span> <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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4
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5
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--minversion</span> 20130222 <span class="o" style="font-weight: 600;">></span> /dev/null <span class="o" style="font-weight: 600;">||</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span>: warning: old version of parallel, might be slow 1>&2</span>
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7
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"></span>
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8
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># use a record size of 8 lines, so that paired sequences stay together:</span></span>
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9
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>parallel <span class="nt" style="color: #000080;">--gnu</span> <span class="nt" style="color: #000080;">--pipe</span> <span class="nt" style="color: #000080;">-L8</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre></td>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>parallel <span class="nt" style="color: #000080;">--round</span> <span class="nt" style="color: #000080;">-L8</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#062baa88bb03951a036716bb1775a09eade2439e"><strong>build/seed-doc.sh</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,14 +56,14 @@ do</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> grep</span> <span class="s1" style="color: #d14;">'^# '</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span><span class="s1" style="color: #d14;">' '</span> <span class="nt" style="color: #000080;">-f2-</span></span>
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57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>It uses this seed alphabet::</span>
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58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="new_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> awk</span> <span class="s1" style="color: #d14;">'!/^#/ && NF > 1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^/ /'</span></span>
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> awk</span> <span class="s1" style="color: #d14;">'!/^#/ && NF > <span class="idiff left right addition">1 && length($1) == </span>1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^/ /'</span></span>
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60
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60
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span></span>
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61
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<td class="new_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'NF == 1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-<span class="idiff left right deletion">l</span></span><span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> 1 <span class="o" style="font-weight: 600;">]</span></span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'<span class="idiff left addition">!/^#/ && length($1) > 1 || </span>NF == 1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-<span class="idiff right addition">w</span></span><span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">=</span> 1 <span class="o" style="font-weight: 600;">]</span></span>
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62
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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
62
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then </span><span class="nb" style="color: #0086b3;">echo </span>And this pattern::</span>
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63
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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
63
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else </span><span class="nb" style="color: #0086b3;">echo </span>And these patterns::</span>
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64
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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65
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="new_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> awk</span> <span class="s1" style="color: #d14;">'NF == 1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^/ /'</span></span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> awk</span> <span class="s1" style="color: #d14;">'<span class="idiff left right addition">!/^#/ && length($1) > 1 || </span>NF == 1'</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^/ /'</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s1" style="color: #d14;">'^#lastdb'</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>It sets this lastdb default:</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#c08354c0b0830a059880a852680dec5f7003bfb8"><strong>data/RY16-8.seed</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">@@ -3,7 +3,7 @@</td>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#abbreviation RY16</span>
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5
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#lastal -r6 -q18 -a21 -b9</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#lastal <span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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7
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">R A G</span>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Y C T</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#f2751d8625d2277c99120885eaad1a35aceef91d"><strong>data/RY32-10.seed</strong></a>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#abbreviation RY32</span>
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#lastal -r6 -q18 -a21 -b9</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#lastal <span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">R A G</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Y C T</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#d4865a426f82cbe8dc69174553ff32a71d5fc7b8"><strong>data/RY4-6.seed</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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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">#abbreviation RY4</span>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#lastal -r6 -q18 -a21 -b9</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#lastal <span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">R A G</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Y C T</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#ff2c3344642495a5d57dfe6c736ac9785228e4f9"><strong>data/RY8-8.seed</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">@@ -3,7 +3,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#abbreviation RY8</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#lastal -r6 -q18 -a21 -b9</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#lastal <span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">R A G</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Y C T</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (1296-1) unstable; urgency=medium</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 1296</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Bump Standards-Version to 4.6.1 (no changes needed)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sun, 29 May 2022 19:12:57 +0530</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">last-align (1282-1) unstable; urgency=medium</span>
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version 1282</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libsimde-dev,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> debhelper</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.6.<span class="idiff left right deletion">0</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.6.<span class="idiff left right addition">1</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/last-align</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/last-align.git</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: https://gitlab.com/mcfrith/last</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#6da0343fd1e96c9faaa35ff4e058c0bb04191144"><strong>doc/last-cookbook.rst</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">@@ -145,47 +145,53 @@ you expect the rates to be roughly the same.</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext">Aligning high-indel-error long DNA reads to a genome</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">----------------------------------------------------</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">Suppose we have DNA reads in either FASTA or FASTQ_ format. <span class="idiff left right deletion">This is</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"><span class="idiff left right deletion">sensitive but slow</span>::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">Suppose we have DNA reads in either FASTA or FASTQ_ format. <span class="idiff left right addition">We can</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"><span class="idiff left right addition">align them to a genome like this</span>::</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> lastdb -P8 -u<span class="idiff left right deletion">NEAR</span> mydb genome.fa</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> lastdb -P8 -u<span class="idiff left right addition">RY4</span> mydb genome.fa</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> last-train -P8 -Q0 mydb reads.fastq > reads.train</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"> lastal -P8 -p reads.train mydb reads.fastq | last-split > out.maf</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext">``-P8`` makes it faster by running 8 parallel threads, adjust as</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext">appropriate for your computer. This has no effect on the results.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext">``-u<span class="idiff left deletion">NEAR</span>`` selects a `seeding scheme`_ that<span class="idiff right deletion">'s better at finding</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"><span class="idiff left right deletion">alignments with few substitutions and/or many gaps</span>.</span>
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158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">``-u<span class="idiff left addition">RY4</span>`` selects a `seeding scheme`_ that<span class="idiff right addition"> reduces the run time and</span></span>
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159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"><span class="idiff left right addition">memory use, but also reduces sensitivity</span>.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext">``-Q0`` makes it discard the fastq_ quality information (or you can</span>
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext">keep-but-ignore it with ``-Qkeep``).</span>
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"></span>
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164
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">last-split_ <span class="idiff left deletion">finds a unique be</span>st<span class="idiff deletion"> </span>al<span class="idiff right deletion">ignment for each part of each read.</span></span>
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165
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"><span class="idiff left right deletion">It gives each alignment a `mismap probability`_, which is high if that</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"><span class="idiff left deletion">part of the read is almost equally similar to several</span> part<span class="idiff right deletion">s</span> of the</span>
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167
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext">genome.</span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">last-split_ <span class="idiff left addition">cuts the output of ``la</span>stal<span class="idiff right addition">`` down to a unique best</span></span>
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165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"><span class="idiff left right addition">alignment for each part of each read. It gives each alignment a</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"><span class="idiff left addition">`mismap probability`_, which is high if that</span> part of the<span class="idiff right addition"> read is</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"><span class="idiff left right addition">almost equally similar to several parts of the </span>genome.</span>
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168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">Here we didn't suppress alignments caused by simple sequence (like</span>
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170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">``cacacacacacacacacacacaca``), so as not to hide anything from</span>
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171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">last-split_. You can discard such alignments with last-postmask_</span>
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172
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext">(though they may help to explain each part of a DNA read).</span>
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173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"></span>
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174
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"><span class="idiff left right deletion">You can go faster by sacrificing a bit of sensitivity. It depends on</span></span>
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175
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<td class="new_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext"><span class="idiff left deletion">your aim, e.g. slow-and-sensitive seems necessary to</span> find<span class="idiff deletion"> </span>in<span class="idiff right deletion">tricate</span></span>
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176
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext"><span class="idiff left right deletion">rearrangements of repeats. Suggested ways to go faster:</span></span>
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174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"><span class="idiff left right addition">To make it more sensitive but slow, replace ``RY4`` with ``NEAR``:</span></span>
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175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"><span class="idiff left addition">good for smaller data. (``-uNEAR`` is suitable for</span> findin<span class="idiff right addition">g alignments</span></span>
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176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"><span class="idiff left right addition">with few substitutions and/or many gaps.)</span></span>
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177
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177
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"></span>
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178
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext">* `Mask repeats`_. This has often worked well.</span>
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178
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">Aligning low-error long DNA reads to a genome</span>
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179
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">We can do this the same way as for high-error reads, but perhaps</span>
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182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">accelerate more aggressively. ``RY8`` reduces the run time and memory</span>
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183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">use even more than ``RY4``. (This is because ``RY8`` uses ~1/8 of the</span>
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184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">seeds, i.e. initial matches, whereas ``RY4`` uses ~1/4). ``RY16`` is</span>
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185
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">faster still, and ``RY32`` is the fastest of these options.</span>
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179
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186
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"></span>
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180
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<td class="new_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext">* Add lastal_ option ``-k8`` (or ``-k16`` etc). This makes it faster,</span>
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181
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> by only finding initial matches starting at every 8th (or 16th etc)</span>
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182
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> position in the reads.</span>
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187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">Also, lastal_ option ``-C2`` may reduce run time with little effect on</span>
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188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">accuracy.</span>
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183
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189
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext"></span>
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184
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<td class="new_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"><span class="idiff left deletion">* Re</span>pl<span class="idiff deletion">a</span>ce<span class="idiff right deletion"> ``-uNEAR`` with ``-uRY32`` (or ``-uRY16``, ``-uRY8``,</span></span>
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185
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"><span class="idiff left right deletion"> ``-uRY4``). This makes it check for initial matches starting at</span></span>
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186
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"><span class="idiff left right deletion"> only ~1/32 (or ~1/16 etc) of positions, in both reads and genome.</span></span>
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187
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"><span class="idiff left right deletion"> Compared to ``-k``: this harms sensitivity slightly more, but</span></span>
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188
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext"><span class="idiff left right deletion"> reduces memory use and makes lastdb faster.</span></span>
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190
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"><span class="idiff left addition">Aligning potentially-s</span>pl<span class="idiff addition">i</span>ce<span class="idiff right addition">d RNA or cDNA long reads to a genome</span></span>
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191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"><span class="idiff left right addition">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"><span class="idiff left right addition">See here_. (For low-error reads, you can probably omit ``-d90`` and</span></span>
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194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"><span class="idiff left right addition">``-m20``.)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">Which genome version to use?</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" 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">@@ -198,22 +204,7 @@ like "analysis set".</td>
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198
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext">You can use multiple genomes, which will be treated like one big</span>
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199
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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">genome::</span>
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200
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206
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"></span>
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201
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> lastdb -P8 -uNEAR mydb human.fa virus.fa other-genomes.fa</span>
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202
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203
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">Aligning low-error long DNA reads to a genome</span>
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204
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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205
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206
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">We can do this the same way as for high-error reads, but perhaps</span>
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207
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">accelerate more aggressively (e.g. ``-uRY32``).</span>
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208
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"></span>
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209
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">If repeats are not masked, lastal_ option ``-C2`` may reduce run time</span>
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210
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext">with little effect on accuracy.</span>
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211
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212
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext">Aligning potentially-spliced RNA or cDNA long reads to a genome</span>
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213
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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214
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext">See here_. (For low-error reads, you can probably omit ``-d90`` and</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext">``-m20``.)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> lastdb -P8 -uRY4 mydb human.fa virus.fa other-genomes.fa</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">Aligning Illumina DNA reads to a genome</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" 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">@@ -235,7 +226,7 @@ didn't use this option.)</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC227" class="line" lang="plaintext">This recipe may be excessively slow-and-sensitive. Adding lastal_</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC228" class="line" lang="plaintext">option ``-C2`` may make it faster with negligible accuracy loss. You</span>
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238
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext">can accelerate with e.g. ``-uRY16`` <span class="idiff left right deletion">or ``-k16`` </span>as above.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">can accelerate with e.g. ``-uRY16`` as above.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC230" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext">Finding very short DNA alignments</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC232" 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">@@ -306,7 +297,7 @@ Finally, we can make a dotplot_::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC297" class="line" lang="plaintext"> last-dotplot humchi2.maf humchi2.png</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC298" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC299" class="line" lang="plaintext">**To go faster** with minor accuracy loss: replace ``-uNEAR`` with</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext">``-uRY32``<span class="idiff left right deletion"> and/or `mask repeats`_</span>.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">``-uRY32``.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC302" class="line" lang="plaintext">To squeeze out the last 0.000...1% of accuracy: add ``-m50`` to the</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext">lastal_ options.</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">@@ -328,7 +319,7 @@ consider using 5-byte LAST (lastdb5_ and lastal5_). Ordinary (4-byte)</td>
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328
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC319" class="line" lang="plaintext">LAST can't handle so much sequence at once, so lastdb_ splits it into</span>
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329
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC320" class="line" lang="plaintext">"volumes", which may be inefficient. 5-byte LAST avoids voluming, but</span>
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330
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext">uses more memory. So lastdb5_ works well with a memory-reducing</span>
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331
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext">option<span class="idiff left deletion">:</span> ``-uRY`` or ``-w``<span class="idiff right deletion"> or ``-W``</span>.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">option<span class="idiff left right addition"> such as</span> ``-uRY`` or ``-w``.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC324" class="line" lang="plaintext">Moar faster</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext">-----------</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#1bbcf798dd6c7dc9ad18596c421c40c0196ed866"><strong>doc/last-map-probs.rst</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">@@ -49,16 +49,6 @@ Details</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> (e.g. because there are no lines starting with "# batch"), it might</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> need too much memory.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">Using multiple CPUs</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">-------------------</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">This will run the pipeline on all your CPU cores::</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> parallel-fastq "lastal -Q1 -D1000 hu | last-map-probs" < reads.fastq > myalns.maf</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">It requires GNU parallel to be installed</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">(http://www.gnu.org/software/parallel/).</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">Limitations</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">-----------</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#ddeca73099d2ddf58518033faefe70ad37b8745d"><strong>doc/last-parallel.rst</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ Running LAST in parallel</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">========================</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">You can make LAST faster by running it on multiple CPUs / cores. The</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">easiest way is with lastal's -P option::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">easiest way is with lastal<span class="idiff left right addition">_</span>'s -P option::</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> lastal -P4 my-index queries.fasta > out.maf</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" 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">@@ -15,7 +15,7 @@ This works by aligning different query sequences in different threads</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Dealing with very long query sequences</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">--------------------------------------</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">lastal aligns one "batch" of queries at a time, so if the batch has</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">lastal<span class="idiff left right addition">_</span> aligns one "batch" of queries at a time, so if the batch has</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">only one query you won't get any parallelization. This can be fixed</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">by increasing the batch size, with option -i::</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" 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">@@ -31,50 +31,52 @@ If you have a multi-command "pipeline", such as::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> lastal -P4 my-index queries.fasta | last-split > out.maf</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">then the -P option may help, because lastal is often the slowest step,</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">but it would be nice to parallelize the whole thing. Unfortunately,</span>
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">last-split doesn't have a -P option, and even if it did, the pipe</span>
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">between the commands would become a bottleneck.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">then the ``-P`` option may help, because lastal is often the slowest</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">step, but it would be nice to parallelize the whole thing.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">You can use parallel-fasta and parallel-fastq (which accompany LAST,</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">but require `GNU parallel`_ to be installed). These commands read</span>
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<td class="new_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">sequence data, split it into blocks (with a whole number of sequences</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">per block), and run the blocks in parallel through any command or</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">pipeline you specify, using all your CPU cores. Here are some</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">examples.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">You can use ``parallel-fasta`` and ``parallel-fastq``, which accompany</span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">LAST, but require `GNU Parallel`_ to be installed.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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40
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Instead of this::</span>
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47
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41
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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48
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> lastal <span class="idiff left right deletion">mydb queries.fa > myalns</span>.maf</span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> lastal <span class="idiff left right addition">-P8 -p my.train mydb seqs.fasta | last-split > out</span>.maf</span>
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49
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43
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">try this::</span>
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45
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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52
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> parallel-fasta "lastal <span class="idiff left right deletion">mydb" < queries.fa > myalns</span>.maf</span>
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46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> parallel-fasta <span class="idiff left addition">-j8 </span>"lastal <span class="idiff right addition">-p my.train mydb | last-split" < seqs.fasta > out</span>.maf</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>
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48
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Instead of this::</span>
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49
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> lastal -<span class="idiff left right deletion">Q1 db q</span>.fastq | last-split > out.maf</span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> lastal -<span class="idiff left addition">P8 -p my.train mydb seqs</span>.fastq<span class="idiff addition">.gz</span> | last-split <span class="idiff addition">| gzip </span>> out.maf<span class="idiff right addition">.gz</span></span>
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57
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51
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">try this::</span>
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59
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53
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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60
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> parallel-fastq "lastal -<span class="idiff left deletion">Q1 </span>db | last-split<span class="idiff right deletion">" < q.fastq</span> > out.maf</span>
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54
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> <span class="idiff left addition">zcat seqs.fastq.gz | </span>parallel-fastq <span class="idiff addition">-j8 </span>"lastal -<span class="idiff addition">p my.train my</span>db | last-split<span class="idiff addition"> | gzip"</span> > out.maf<span class="idiff right addition">.gz</span></span>
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61
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55
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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62
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">Instead of this::</span>
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63
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56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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64
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"><span class="idiff left right deletion"> bzcat queries.fa.bz2 | lastal mydb > myalns.maf</span></span>
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57
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"><span class="idiff left right addition">Notes:</span></span>
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65
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58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"></span>
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66
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">try this::</span>
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">* ``parallel-fasta`` and ``parallel-fastq`` simply run GNU Parallel</span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> with a few options for fasta or fastq: you can specify other GNU</span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> Parallel options (like ``-j8``).</span>
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67
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62
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>
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68
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<td class="new_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> bzcat queries.fa.bz2 | parallel-fasta "lastal mydb" > myalns.maf</span>
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63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">* The ``gzip`` example above runs ``gzip`` several times in parallel,</span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> and concatenates the results. Fortunately, that is valid ``gz``</span>
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65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> format.</span>
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69
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66
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></span>
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70
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<td class="new_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">Notes:</span>
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67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">* ``lastal`` reads the ``mydb`` files into shared memory, so this</span>
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68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> memory use does not get mutiplied 8 times.</span>
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71
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69
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>
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72
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">* parallel-fasta and parallel-fastq simply execute GNU parallel with a</span>
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73
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> few options for fasta or fastq: you can specify other GNU parallel</span>
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74
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> options to control the number of simultaneous jobs, use remote</span>
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75
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> computers, get the output in the same order as the input, etc.</span>
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70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">* ``parallel-fastq`` assumes that each fastq record is 4 lines, so</span>
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71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> there should be no line wrapping or blank lines. (Actually, it</span>
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> assumes one "record" is 8 lines, to keep paired reads together.)</span>
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76
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73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>
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77
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">* parallel-fastq assumes that each fastq record is 4 lines, so there</span>
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78
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<td class="new_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> should be no line wrapping or blank lines.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">* In the current version, ``parallel-fasta`` and ``parallel-fastq``</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> use GNU Parallel's ``--round`` option. This avoids the overhead of</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> restarting the command for each input chunk, but it prevents keeping</span>
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77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> the order of sequences, and stashes the output in large temporary</span>
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78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> files. If necessary, use ``$TMPDIR`` or ``--tmpdir`` to choose a</span>
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79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> temp directory with enough space.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.. _lastal: doc/lastal.rst</span>
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80
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">.. _GNU parallel: http://www.gnu.org/software/parallel/</span></pre></td>
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<li id="977fadb853a729d73f897f1532ab693a2edb5af2">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#977fadb853a729d73f897f1532ab693a2edb5af2"><strong>doc/last-seeds.rst</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">@@ -206,7 +206,7 @@ And these patterns::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"> YYYYRY</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext">It sets this lastal default:</span>
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209
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext">-r6 -q18 -a21 -b9</span>
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209
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"><span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">RY8-8 (abbreviation: RY8)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">-------------------------</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -254,7 +254,7 @@ And these patterns::</td>
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254
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"> YYYYYYYR</span>
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255
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext"></span>
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256
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext">It sets this lastal default:</span>
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257
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<td class="new_line diff-line-num old" 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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext">-r6 -q18 -a21 -b9</span>
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257
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"><span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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258
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258
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext">RY16-8 (abbreviation: RY16)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC260" 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">@@ -286,7 +286,7 @@ And these patterns::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC286" class="line" lang="plaintext"> YYRRYRYY</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC288" class="line" lang="plaintext">It sets this lastal default:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">-r6 -q18 -a21 -b9</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"><span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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290
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext">RY32-10 (abbreviation: RY32)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC292" 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">@@ -334,5 +334,5 @@ And these patterns::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext"> YYYYYYRRRY</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC336" class="line" lang="plaintext">It sets this lastal default:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext">-r6 -q18 -a21 -b9</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"><span class="idiff left right addition">-m2 </span>-r6 -q18 -a21 -b9</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#3df0be4654dc98e9c961572d8d1876b21024c1d2"><strong>doc/maf-cut.rst</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">@@ -17,4 +17,14 @@ You can omit the sequence name::</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Then, the range applies to the topmost sequence in each alignment.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">``maf-cut`` can also get parts of sequences::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> maf-cut chr7:1234000-1235000 alignments.maf sequences.fasta</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">This first applies ``maf-cut`` to ``alignments.maf`` in the usual way</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">(without printing anything). For each sequence, it gets the minimum</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">start coordinate and maximum end coordinate in the resulting</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">alignments. It prints this segment of each sequence in</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">``sequences.fasta``. (fastq format is ok too.)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">.. _MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5</span></pre></td>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#d0552713235c86a577163a3f58b56207610ad394"><strong>src/CyclicSubsetSeed.cc</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">@@ -86,47 +86,50 @@ n ACGT\n\</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">patterns</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextPattern</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;">istream</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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span> <span class="p">){</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">getline</span><span class="p">(</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">pattern</span> <span class="p">)</span> <span class="p">){</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC93" 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;">istringstream</span> <span class="n" style="color: #333;">iss</span><span class="p">(</span> <span class="n" style="color: #333;">pattern</span> <span class="p">);</span></span>
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94
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC94" 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;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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95
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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96
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">x</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="sc" style="color: #d14;">'#'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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97
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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98
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">)</span> <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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99
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">x</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="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"bad seed line: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pattern</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">pattern</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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102
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<td class="new_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">lineType</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC90" 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;">istringstream</span> <span class="n" style="color: #333;">s</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC91" 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;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">x</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="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">// blank or comment line</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="c1" style="color: #998; font-style: italic;">// seed-alphabet line</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <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;">// seed-pattern line</span></span>
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103
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96
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="p">}</span></span>
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104
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97
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>
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105
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<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left deletion">size_t</span></span><span class="idiff deletion"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">findSeedLetter</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="idiff deletion"> </span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>&</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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106
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<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="idiff left deletion"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">seedLetter</span><span class="idiff right deletion"> </span><span class="p">){</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;"><span class="idiff left addition">const</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">char</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">*</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">letterGroups</span></span><span class="p"><span class="idiff addition">(</span></span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;"><span class="idiff addition">></span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff right addition">&</span></span><span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="idiff left addition"> </span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">seedLetter</span><span class="p">)</span><span class="idiff right addition"> </span><span class="p">{</span></span>
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107
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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// go backwards, so that newer definitions override older ones:</span></span>
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108
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC108" 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;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</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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109
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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110
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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111
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC111" 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;">s</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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112
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<td class="new_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">s</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;">seedLetter</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" 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="n" style="color: #333;">seedAlphabet</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</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;">seedLetter</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</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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113
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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<td class="new_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="idiff left deletion"> </span><span class="s" style="color: #d14;">"unknown symbol in seed pattern: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">seedLetter</span><span class="p">)</span><span class="idiff right deletion"> </span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">ERR</span><span class="p">(</span><span class="s" style="color: #d14;">"unknown symbol in seed pattern: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">seedLetter</span><span class="p">));</span></span>
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115
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106
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="p">}</span></span>
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116
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107
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"></span>
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117
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">init</span><span class="p">(</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">letterCode</span><span class="p">[],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mainSequenceAlphabet</span> <span class="p">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
123
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC123" 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;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span> <span class="p">){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
124
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">seedLetter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
125
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">isspace</span><span class="p">(</span><span class="n" style="color: #333;">seedLetter</span><span class="p">)</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
126
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<td class="new_line diff-line-num 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findSeedLetter</span><span class="p">(</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span> <span class="n" style="color: #333;">seedLetter</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC127" 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;">istringstream</span> <span class="n" style="color: #333;">iss</span><span class="p">(</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">);</span></span>
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128
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">iss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">seedLetter</span><span class="p">;</span></span>
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129
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">appendPosition</span><span class="p">(</span> <span class="n" style="color: #333;">iss</span><span class="p">,</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span> <span class="n" style="color: #333;">letterCode</span><span class="p">,</span> <span class="n" style="color: #333;">mainSequenceAlphabet</span> <span class="p">);</span></span>
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108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addPatterns</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;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">patterns</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span></span>
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111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">letterCode</span><span class="p">[],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mainSequenceAlphabet</span><span class="p">)</span> <span class="p">{</span></span>
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113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">;</span></span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">word</span><span class="p">;</span></span>
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115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" 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;">istringstream</span> <span class="n" style="color: #333;">textStream</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">);</span></span>
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116
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">textStream</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineType</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</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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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" 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;">istringstream</span> <span class="n" style="color: #333;">lineStream</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">lineStream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">word</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">CyclicSubsetSeed</span> <span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" 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;">word</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" 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;">istringstream</span> <span class="n" style="color: #333;">s</span><span class="p">(</span><span class="n" style="color: #333;">letterGroups</span><span class="p">(</span><span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span> <span class="n" style="color: #333;">word</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">pat</span><span class="p">.</span><span class="n" style="color: #333;">appendPosition</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span> <span class="n" style="color: #333;">letterCode</span><span class="p">,</span></span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">mainSequenceAlphabet</span><span class="p">);</span></span>
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129
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">patterns</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pat</span><span class="p">);</span></span>
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131
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133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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134
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#38e88d72aa956d3886597351d58b37469947a653"><strong>src/CyclicSubsetSeed.hh</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,21 +72,16 @@ public:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// codes. Finally, "@" allows any match or transition.</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">stringFromDnaPatterns</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">patterns</span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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75
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Reads lines from "in" until it finds a pattern line. Any seed</span></span>
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76
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// alphabet lines are appended to "seedAlphabet". If it finds a</span></span>
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77
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pattern line, it stores it in "pattern" and returns true, else it</span></span>
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78
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// returns false. Blank lines and comment lines starting with # are</span></span>
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79
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ignored.</span></span>
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80
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">nextPattern</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;">istream</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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81
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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82
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">subsetLists</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">subsetMaps</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">originalSubsetMaps</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfSubsetsPerPosition</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read subset-seed patterns from text and add them to patterns.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The text should start with lines defining a seed alphabet,</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// followed by lines with seed patterns. Blank lines and comment</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// lines starting with # are ignored. Seed letters are</span></span>
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79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// case-sensitive.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <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;">addPatterns</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;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">patterns</span><span class="p">,</span></span>
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81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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82
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">letterCode</span><span class="p">[],</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mainSequenceAlphabet</span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">swap</span><span class="p">(</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">x</span> <span class="p">){</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">subsetLists</span><span class="p">.</span><span class="n" style="color: #333;">swap</span><span class="p">(</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">subsetLists</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">@@ -95,13 +90,6 @@ public:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfSubsetsPerPosition</span><span class="p">.</span><span class="n" style="color: #333;">swap</span><span class="p">(</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">numOfSubsetsPerPosition</span> <span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Seed letters are case-sensitive.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC99" class="line" lang="cpp"> <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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="n" style="color: #333;">letterCode</span><span class="p">[],</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mainSequenceAlphabet</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// "inputLine" should be a grouping of sequence letters.</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">appendPosition</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;">istream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">inputLine</span><span class="p">,</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMaskLowercase</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</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">@@ -172,7 +172,7 @@ Miscellaneous options (default settings):\n\</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="s" style="color: #d14;">-C: omit gapless alignments in >= C others with > score-per-length (off)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"><span class="s" style="color: #d14;">-P: number of parallel threads ("</span></span>
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174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">numOfThreads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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175
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"><span class="s" style="color: #d14;">-i: query batch size (<span class="idiff left right deletion">8 KiB, unless there is > 1 thread or lastdb volume</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"><span class="s" style="color: #d14;">-i: query batch size (<span class="idiff left right addition">64M if multi-volume, else 32M if multi-thread, else 8K</span>)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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176
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176
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"><span class="s" style="color: #d14;">-M: find minimum-difference alignments (faster but cruder)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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177
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177
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="s" style="color: #d14;">-T: type of alignment: 0=local, 1=overlap ("</span></span>
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178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stringify</span><span class="p">(</span><span class="n" style="color: #333;">globality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); 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="524" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -524,7 +524,10 @@ void LastalArguments::setDefaultsFromAlphabet( bool isDna, bool isProtein,</td>
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524
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524
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">outputType</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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525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x1000000</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 16 Mbytes</span></span>
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526
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isVolumes</span> <span class="p">)</span></span>
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527
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<td class="new_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x800000</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 8 Mbytes</span></span>
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527
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x2000000</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 32 Mbytes</span></span>
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528
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 32 Mbytes gave quite good load-balancing when aligning human</span></span>
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529
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// nanopore reads with 16 threads. Sometimes 64M (and even 128M)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
530
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// was better. With WindowMasker, smaller batches were fine.</span></span>
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528
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531
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">inputFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sequenceFormat</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prb</span> <span class="p">)</span></span>
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529
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532
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x2000000</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 32 Mbytes (?)</span></span>
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533
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#b8ecac13f5a049cde8c83663390da1d0fc2bd9a1"><strong>src/fileMap.cc</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">@@ -25,8 +25,7 @@ static void err( const std::string& s ) {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// random access can be horribly slow (at least on two Linux 2.6</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// systems).</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">primeMemory</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="n" style="color: #333;">begin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bytes</span> <span class="p">){</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use "static" to stop the compiler optimizing the whole function away:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">stepSize</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">begin</span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">bytes</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">stepSize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">stepSize</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">@@ -34,6 +33,8 @@ static void primeMemory( void* begin, size_t bytes ){</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">stepSize</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">dontOptimizeMeAway</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</span><span class="p">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">dontOptimizeMeAway</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dontOptimizeMeAway</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// ??? prevents compiler warning</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cbrc</span><span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#de4252990d12a909e50ff0b994d1715eae0ea5fd"><strong>src/lastdb.cc</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">@@ -51,49 +51,36 @@ bool isDubiousDna( const Alphabet& alph, const MultiSequence& multi ){</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</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" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addSeeds</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;">CyclicSubsetSeed</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seeds</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seedText</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastdbArguments</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span> <span class="p">){</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" 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;">istringstream</span> <span class="n" style="color: #333;">iss</span><span class="p">(</span> <span class="n" style="color: #333;">seedText</span> <span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" 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;">pattern</span><span class="p">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextPattern</span><span class="p">(</span> <span class="n" style="color: #333;">iss</span><span class="p">,</span> <span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span> <span class="n" style="color: #333;">pattern</span> <span class="p">)</span> <span class="p">){</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">CyclicSubsetSeed</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">seedAlphabet</span><span class="p">,</span> <span class="n" style="color: #333;">pattern</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isCaseSensitive</span><span class="p">,</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Set up the seed pattern(s)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeSubsetSeeds</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;">CyclicSubsetSeed</span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seeds</span><span class="p">,</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seedText</span><span class="p">,</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LastdbArguments</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span><span class="p">,</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alph</span> <span class="p">){</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span><span class="p">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCaseSens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isCaseSensitive</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" 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;">args</span><span class="p">.</span><span class="n" style="color: #333;">subsetSeedFile</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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76
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<td class="new_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion">addSeed</span>s</span><span class="p">(</span><span class="idiff deletion"> </span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">seedText</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff deletion">args</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">alph</span></span><span class="idiff right deletion"> </span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left addition">CyclicSubsetSeed</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">::</span></span><span class="n" style="color: #333;"><span class="idiff addition">addPattern</span>s</span><span class="p">(</span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">seedText</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff addition">isCaseSens</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">alph</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">encode</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">a</span></span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">dnaSeedPatterns</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" 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;">x</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;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">dnaSeedPatterns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">dnaSeedPatterns</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">];</span></span>
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81
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" 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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromDnaPatterns</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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82
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<td class="new_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion">addSeeds</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">seeds</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">s</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">args</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff right deletion">alph</span></span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left addition">CyclicSubsetSeed</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">::</span></span><span class="n" style="color: #333;"><span class="idiff addition">addPatterns</span></span><span class="p"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff addition">seeds</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">s</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">isCaseSens</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">alph</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">encode</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">a</span></span><span class="p">);</span></span>
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83
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70
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="p">}</span></span>
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84
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71
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="p">}</span></span>
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85
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">seedPatterns</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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86
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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" 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;">unsigned</span> <span class="n" style="color: #333;">x</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;">x</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">seedPatterns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">x</span> <span class="p">){</span></span>
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87
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74
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">seedPatterns</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">];</span></span>
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88
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<td class="new_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" 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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromPatterns</span><span class="p">(</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="p">);</span></span>
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89
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<td class="new_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion">addSeed</span>s</span><span class="p">(</span><span class="idiff deletion"> </span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff deletion">args</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">alph</span></span><span class="idiff right deletion"> </span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left addition">CyclicSubsetSeed</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">::</span></span><span class="n" style="color: #333;"><span class="idiff addition">addPattern</span>s</span><span class="p">(</span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff addition">isCaseSens</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">alph</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">encode</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">a</span></span><span class="p">);</span></span>
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90
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="p">}</span></span>
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92
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<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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93
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80
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" 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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">letters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alph</span><span class="p">.</span><span class="n" style="color: #333;">dna</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
94
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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromName</span><span class="p">(</span> <span class="s" style="color: #d14;">"YASS"</span> <span class="p">)</span></span>
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95
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
82
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">CyclicSubsetSeed</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringFromPatterns</span><span class="p">(</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="p">);</span></span>
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96
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left deletion">addSeed</span>s</span><span class="p">(</span><span class="idiff deletion"> </span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff deletion">args</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">alph</span></span><span class="idiff right deletion"> </span><span class="p">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left addition">CyclicSubsetSeed</span></span><span class="o" style="font-weight: 600;"><span class="idiff addition">::</span></span><span class="n" style="color: #333;"><span class="idiff addition">addPattern</span>s</span><span class="p">(</span><span class="n" style="color: #333;">seeds</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff addition">isCaseSens</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">alph</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">encode</span></span><span class="p"><span class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">a</span></span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">)</span> <span class="n" style="color: #333;">ERR</span><span class="p">(</span> <span class="s" style="color: #d14;">"no seed patterns"</span> <span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>
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143
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143
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC143" class="line" lang="make"> ../build/mat-inc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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144
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144
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC144" class="line" lang="make"></span>
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145
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION1</span> <span class="o" style="font-weight: 600;">=</span> git describe <span class="nt" style="color: #000080;">--dirty</span></span>
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146
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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right deletion">82</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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146
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right addition">96</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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147
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC147" class="line" lang="make"></span>
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148
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> ../.git <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(VERSION1)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$(VERSION2)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>
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149
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#6c90adec85ff9834658c43a287e5d780f52732ef"><strong>test/last-test.out</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">@@ -5235,8 +5235,8 @@ s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATA</td>
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5235
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5235
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5236
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5236
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5236" class="line" lang=""># Query sequences=1 normal letters=485</span>
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5237
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5237
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5237" class="line" lang="">#</span>
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5238
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<td class="new_line diff-line-num old" data-linenumber="5238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5238" class="line" lang=""># a=21 b=4 A=21 B=4 e=114 d=7<span class="idiff left right deletion">0</span> x=113 y=49 z=113 D=1e+06 E=2.92797e+07</span>
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5239
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<td class="new_line diff-line-num old" data-linenumber="5238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5239" class="line" lang=""># R=01 u=0 s=2 S=0 M=0 T=0 m=<span class="idiff left deletion">10</span> l=1 n=<span class="idiff right deletion">10</span> k=1 w=1000 t=4.88281 j=3 Q=0</span>
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5238
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5238" class="line" lang=""># a=21 b=4 A=21 B=4 e=114 d=7<span class="idiff left right addition">7</span> x=113 y=49 z=113 D=1e+06 E=2.92797e+07</span>
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5239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5239" class="line" lang=""># R=01 u=0 s=2 S=0 M=0 T=0 m=<span class="idiff left addition">2</span> l=1 n=<span class="idiff right addition">2</span> k=1 w=1000 t=4.88281 j=3 Q=0</span>
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5240
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5240
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5240" class="line" lang=""># /tmp/last-test</span>
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5241
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5241
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5241" class="line" lang=""># Reference sequences=1 normal letters=16571</span>
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5242
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5242
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5242" class="line" lang=""># lambda=0.201859 K=0.288737</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5275" style="width: 35px; color: rgba(0,0,0,0.3); 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="5275" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5275,7 +5275,6 @@ s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATA</td>
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5275
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<td class="new_line diff-line-num" data-linenumber="5275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5275
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5275" class="line" lang="">644 chrM 1742 311 + 16571 chrM 2432 326 + 16775 18,1:0,2,0:2,17,0:4,25,0:4,11,0:2,57,1:0,42,0:1,24,0:3,83,0:4,6,3:0,21 EG2=1e-39 E=5.5e-49</span>
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5276
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<td class="new_line diff-line-num" data-linenumber="5276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5276
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5276" class="line" lang="">627 chrM 656 291 + 16571 chrM 1303 296 + 16775 78,0:3,35,0:2,6,2:0,20,0:1,19,0:1,55,1:0,57,0:1,18 EG2=3.1e-38 E=1.7e-47</span>
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5277
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<td class="new_line diff-line-num" data-linenumber="5277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5277
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5277" class="line" lang="">587 chrM 5208 516 + 16571 chrM 5978 522 + 16775 74,0:2,17,2:0,88,0:3,19,3:0,5,5:0,14,0:5,6,3:0,21,0:3,14,1:0,12,2:0,29,0:1,6,0:4,30,0:2,9,0:1,13,1:0,73,0:1,2,0:1,67 EG2=1e-34 E=5.5e-44</span>
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5278
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<td class="new_line diff-line-num old" data-linenumber="5278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5278" class="line" lang="">300 chrM 10642 148 + 16571 chrM 11367 148 + 16775 68,1:0,9,0:1,70 EG2=1.4e-09 E=8e-19</span>
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5279
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5278
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5278" class="line" lang="">288 chrM 8638 216 + 16571 chrM 9353 216 + 16775 216 EG2=1.6e-08 E=9e-18</span>
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5280
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5279
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5279" class="line" lang="">210 chrM 10518 77 + 16571 chrM 11243 77 + 16775 77 EG2=0.11 E=6.2e-11</span>
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5281
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5280
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5280" class="line" lang="">154 chrM 14425 84 + 16571 chrM 16456 84 + 16775 84 EG2=9.1e+03 E=5e-06</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5319" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -5320,18 +5319,3 @@ p $&'~~~~~~~~~~~~(.0233.,,,,,+--&)*+,,,-.-+++++---)'%(+</td>
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5320
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5319
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5319" class="line" lang="">c 20.6 0.00414 1.97 1.05 1.13 4.98 0.158 2.83 0.966 0.0011 9.56 0.997 0.0153 0.0037 1.07 6.54 51.8 16.4 0.361 3 0.27</span>
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5321
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5320
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5322
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5321
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5321" class="line" lang=""># Query sequences=1 normal letters=54</span>
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5323
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5323" class="line" lang="">a score=192 mismap=0.117</span>
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5324
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5324" class="line" lang="">s KI635862 2418195 86 + 12728579 CACAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTC-CGAGCAGCCGG-ATAACAGGCGCGCGCCAC</span>
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5325
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5325" class="line" lang="">s chr1 248803921 88 - 248956422 CATAGCTCACTGCAGCCTTGACCTCCTAGGCTAAAGCAATCCTCCCACCTTAGCCTCTCCAGTAGCTGGAACTACAGGCATGCATCAC</span>
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5326
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5326" class="line" lang="">p #$$%&&'(()******************************************************************************</span>
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5327
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5328
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5328" class="line" lang="">a score=330 mismap=0.75</span>
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5329
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5329" class="line" lang="">s KI636063 409336 105 + 789923 AAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCCATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGCGAGCA</span>
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5330
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5330" class="line" lang="">s chr1 157784 102 + 248956422 aaaataTGGAATGCTTCACAAATTTGCATGTCATTCTTTCACAGAGGCCGTGCCAA---TCTCTCTATTGTTCCAACTTAAGTATGTGTGCTACTGAGGCAAGCA</span>
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5331
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5333" class="line" lang="">a score=203 mismap=0.0127</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5334" class="line" lang="">s KI635862 2418239 48 + 12728579 CAGCCTCAGCCTC-CGAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCC</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#fcd3167fe23623673ee838f0da31855d3d479dff"><strong>test/last-test.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -245,8 +245,6 @@ trap 'rm -f $db*' EXIT</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC245" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># tricky Forward-Backward bug that happened once</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC246" class="line" lang="shell"> lastdb <span class="nv" style="color: #008080;">$db</span> alli.fa</span>
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247
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC247" class="line" lang="shell"> lastal <span class="nt" style="color: #000080;">-j7</span> <span class="nt" style="color: #000080;">-r5</span> <span class="nt" style="color: #000080;">-q5</span> <span class="nt" style="color: #000080;">-a15</span> <span class="nt" style="color: #000080;">-b3</span> <span class="nv" style="color: #008080;">$db</span> huma.fa</span>
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248
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC248" class="line" lang="shell"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC249" class="line" lang="shell"> maf-cut chr1:152413-158286 split1.maf</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC248" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> 2>&1 |</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC249" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> version | diff <span class="nt" style="color: #000080;">-u</span> last-test.out -</span>
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252
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250
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -261,6 +259,7 @@ rm f.* r.*</td>
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261
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259
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC259" class="line" lang="shell">./last-split-test.sh</span>
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262
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260
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC260" class="line" lang="shell">./last-train-test.sh</span>
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263
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261
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC261" class="line" lang="shell">./maf-convert-test.sh</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC262" class="line" lang="shell">./maf-cut-test.sh</span>
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264
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263
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC263" class="line" lang="shell">./maf-swap-test.sh</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC264" class="line" lang="shell"></span>
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266
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC265" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test: lastdb, lastal, last-split, maf-sort, maf-join</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#a279e6bc3648ec4fa6cb7f05adccc78e0c01ad8a"><strong>test/maf-cut-test.out</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">a score=192 mismap=0.117</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">s KI635862 2418195 86 + 12728579 CACAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTC-CGAGCAGCCGG-ATAACAGGCGCGCGCCAC</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">s chr1 248803921 88 - 248956422 CATAGCTCACTGCAGCCTTGACCTCCTAGGCTAAAGCAATCCTCCCACCTTAGCCTCTCCAGTAGCTGGAACTACAGGCATGCATCAC</span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">p #$$%&&'(()******************************************************************************</span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">a score=330 mismap=0.75</span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">s KI636063 409336 105 + 789923 AAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCCATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGCGAGCA</span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">s chr1 157784 102 + 248956422 aaaataTGGAATGCTTCACAAATTTGCATGTCATTCTTTCACAGAGGCCGTGCCAA---TCTCTCTATTGTTCCAACTTAAGTATGTGTGCTACTGAGGCAAGCA</span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">p !"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!</span>
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10
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">a score=203 mismap=0.0127</span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">s KI635862 2418239 48 + 12728579 CAGCCTCAGCCTC-CGAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCC</span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">s chr1 248798136 50 - 248956422 CTGCCTCAGCCTCACAAGTAGCTGGGACTACAGGTGCTTGTCACCACACC</span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">p 33333333333333333333333333333333333322211110.*)'&$</span>
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15
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">@ 7 87 chrMa 141 -</span>
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">TAGTAGGTATGTTTGCTTGTAATATTGAATGTAGGAGCGATAGATAAGAG</span>
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18
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">?:+4>89ABBB@AB?):B=5=1@@49;;9;<9(22+/+>?060.=<4++2</span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">@ 21 87 chrMa 80 +</span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">TTATTATTTATCGTATT</span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">+</span>
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23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">B2BBABBA:1:A8A?=9</span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">@ 95 87 chrMa 131 +</span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">TTATTATTTATCGTATTTACGTTTAATATTATAGGTGAATATATTTATTG</span>
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26
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27
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">> 7 87 chrMa 141 -</span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">TAGTAGGTATGTTTGCTTGTAATATTGAATGTAGGAGCGATAGATAAGAG</span>
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">> 21 87 chrMa 80 +</span>
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">TTATTATTTATCGTATT</span>
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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">> 95 87 chrMa 131 +</span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">TTATTATTTATCGTATTTACGTTTAATATTATAGGTGAATATATTTATTG</span></pre></td>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/04dde6a254a5dacbed8eb4dc37426e605fecc37a...ad07ecda317748675675d73e4a32901e9f0413b3#5f1ef9aa98b3328c3327e88496805261dd201ca8"><strong>test/maf-cut-test.sh</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="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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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span></span>
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4
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>../bin:<span class="nv" style="color: #008080;">$PATH</span></span>
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6
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7
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> maf-cut chr1:152413-158286 split1.maf</span>
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9
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> maf-cut chrM:150-200 bs100.maf bs100.fastq</span>
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11
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'(NR-1) % 4 < 2'</span> bs100.fastq | <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'@'</span> <span class="s1" style="color: #d14;">'>'</span> |</span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> maf-cut chrM:150-200 bs100.maf -</span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> | diff <span class="nt" style="color: #000080;">-u</span> maf-cut-test.out -</span></pre></td>
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