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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/blasr">Debian Med / blasr</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/5850f8a0c22a63fefc3c161aa0f866fdc2e64763">5850f8a0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/28dbe2237a2275a474cd2bf0300c0559cf4ce4d3">28dbe223</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.3.3+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/805b2788eb878c3cea4a900d8ca803b0adafbcc9">805b2788</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.3.3+dfsg'
Update to upstream version '5.3.3+dfsg'
with Debian dir 7b788842dce74d55d929301a77d81145c9a5f962</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/8f3ebf775e1a01f9ae0974e114363f741368c46f">8f3ebf77</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/a54393c09ffa02c8db1ff15f019be452c981f3d6">a54393c0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/1b38236776bd5ec916d3ba5aa8b267074a51a290">1b382367</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:55:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/blasr/commit/869b0124b6fbcd97ca482f5daad79319485f584d">869b0124</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T12:59:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3261916a932aec8d2cae478e6aac183e1e87ea1c">
Blasr.cpp
</a>
</li>
<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#29a9b2356fc2b6abe6c7f29beef1781818296121">
ctest/ecoli.t
</a>
</li>
<li class="file-stats">
<a href="#778536b4a355af646e1a872c49924462e959b335">
<span class="new-file">
+
ctest/long-cigar.t
</span>
</a>
</li>
<li class="file-stats">
<a href="#490d9bbfafbadf3f3e9f14ae4eb510281bafe310">
ctest/meson.build
</a>
</li>
<li class="file-stats">
<a href="#6cb9a3bc27980995c5a30f9048de8d8392d4665c">
ctest/pgc-naive.t
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e58d34221dc60490c30dc9868da14030dd796433">
doc/EXAMPLES.md
</a>
</li>
<li class="file-stats">
<a href="#2e314a0e86c37cb69f20b01ef56cd17a325fd1d5">
iblasr/MappingParameters.h
</a>
</li>
<li class="file-stats">
<a href="#82db61cad929b7cbe4ae3a964d2f67365d4f4d20">
iblasr/RegisterBlasrOptions.h
</a>
</li>
<li class="file-stats">
<a href="#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa">
meson.build
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="3261916a932aec8d2cae478e6aac183e1e87ea1c">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#3261916a932aec8d2cae478e6aac183e1e87ea1c"><strong>Blasr.cpp</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); 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="831" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -831,10 +831,6 @@ int main(int argc, char *argv[])</td>
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831
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<td class="diff-line-num new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BlasrHelp</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
832
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<td class="diff-line-num new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
832
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Not a failure.</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
833
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<td class="diff-line-num new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
833
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
834
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<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">printDiscussion</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
835
</td>
<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BlasrDiscussion</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
836
</td>
<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Not a failure.</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
837
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<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
838
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<td class="diff-line-num new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
834
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
839
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<td class="diff-line-num new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
835
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BlasrConciseHelp</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
840
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<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// A failure.</span></span>
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<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">// Copyright (c) 2014-2015</span>, Pacific Biosciences of California, Inc.</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">// </span>All rights reserved.</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">// </span>Redistribution and use in source and binary forms, with or without</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">// </span>modification, are permitted (subject to the limitations in the</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">// </span>disclaimer below) provided that the following conditions are met:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">// </span> * Redistributions of source code must retain the above copyright</span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">// </span> notice, this list of conditions and the following disclaimer.</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"><span class="idiff left right">// </span> * Redistributions in binary form must reproduce the above</span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">// </span> copyright notice, this list of conditions and the following</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"><span class="idiff left right">// </span> disclaimer in the documentation and/or other materials provided</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"><span class="idiff left right">// </span> with the distribution.</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">// </span> * Neither the name of Pacific Biosciences nor the names of its</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">// </span> contributors may be used to endorse or promote products derived</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"><span class="idiff left right">// </span> from this software without specific prior written permission.</span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">//</span></span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"><span class="idiff left right">// </span>NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE</span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">// </span>GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC</span>
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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"><span class="idiff left right">// </span>BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED</span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">// </span>WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES</span>
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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"><span class="idiff left right">// </span>OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"><span class="idiff left right">// </span>DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS</span>
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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">// </span>CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span>
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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right">// </span>SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT</span>
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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"><span class="idiff left right">// </span>LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"><span class="idiff left right">// </span>USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"><span class="idiff left right">// </span>ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"><span class="idiff left right">// </span>OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"><span class="idiff left right">// </span>OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"><span class="idiff left right">// </span>SUCH DAMAGE.</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">Copyright (c) 2014-2018</span>, Pacific Biosciences of California, Inc.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">All rights reserved.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">modification, are permitted (subject to the limitations in the</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">disclaimer below) provided that the following conditions are met:</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Redistributions of source code must retain the above copyright</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Redistributions in binary form must reproduce the above</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> copyright notice, this list of conditions and the following</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> disclaimer in the documentation and/or other materials provided</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> with the distribution.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * Neither the name of Pacific Biosciences nor the names of its</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> contributors may be used to endorse or promote products derived</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> from this software without specific prior written permission.</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">SUCH DAMAGE.</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,23 +6,15 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">***</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Availability</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="idiff left">The latest release binary can be installed via </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">bioconda</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://bioconda.github.io/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="idiff left">Latest version can be installed via bioconda package </span><span class="sb" style="color: #d14;"><span class="idiff">`blasr`</span></span><span class="idiff right">.</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install -c bioconda blasr</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">Official support is only provided for official and stable</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">SMRT Analysis builds</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.pacb.com/products-and-services/analytical-software/</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">provided by PacBio and not for source builds.</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Unofficial support for binary releases is provided via github issues,</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">not via mail to developers.</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**No**</span> support for source builds; issues will be closed without comment.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Please refer to our <span class="p">[</span><span class="nv" style="color: #008080;">official pbbioconda page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/PacificBiosciences/pbbioconda</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">for information on Installation, Support, License, Copyright, and Disclaimer.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Documentation</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Wiki: all you need to know</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/PacificBiosciences/blasr/wiki</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Running BLASR</span><span class="p">](</span><span class="sx" style="color: #d14;">doc/EXAMPLES.md</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p"> -</span> <span class="p">[</span><span class="nv" style="color: #008080;">Developer environment</span><span class="p">](</span><span class="sx" style="color: #d14;">doc/DEVELOPER.md</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gh" style="color: #999;">DISCLAIMER</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>
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<br>
</li>
<li id="29a9b2356fc2b6abe6c7f29beef1781818296121">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#29a9b2356fc2b6abe6c7f29beef1781818296121"><strong>ctest/ecoli.t</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ Test blasr with --bam</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">rm</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">rf</span> <span class="nv" style="color: #008080;">$OUTDIR</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">ecoli_subset</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span></span>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">BLASR_EXE</span> <span class="nv" style="color: #008080;">$DATDIR</span><span class="sr" style="color: #009926;">/ecoli_subset.fasta $DATDIR/</span><span class="nv" style="color: #008080;">ecoli_reference</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">bam</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">out</span> <span class="nv" style="color: #008080;">$OUTDIR</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">ecoli_subset</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">bam</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">nproc</span> <span class="mi" style="color: #099;">15</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: #008080;">INFO</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="nv" style="color: #008080;">WARNING</span><span class="p">,</span> <span class="nv" style="color: #008080;">BAM</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">PacBio</span> <span class="nv" style="color: #008080;">BAM</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">DATASET</span> <span class="nv" style="color: #008080;">input</span> <span class="nv" style="color: #008080;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">supported</span> <span class="nv" style="color: #008080;">by</span> <span class="nv" style="color: #008080;">PacBio</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: #008080;">INFO</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">SAMTOOLS_EXE</span> <span class="nv" style="color: #008080;">view</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">h</span> <span class="nv" style="color: #008080;">$OUTDIR</span><span class="sr" style="color: #009926;">/ecoli_subset.bam > $OUTDIR/</span><span class="nv" style="color: #008080;">ecoli_subset</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span></span>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#778536b4a355af646e1a872c49924462e959b335"><strong>ctest/long-cigar.t</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="nv" style="color: #008080;">Test</span> <span class="nv" style="color: #008080;">input</span> <span class="nv" style="color: #008080;">query</span> <span class="nv" style="color: #008080;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">pb</span> <span class="nv" style="color: #008080;">bam</span><span class="p">,</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">sam</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">bam</span><span class="p">,</span> <span class="nv" style="color: #008080;">alignment</span> <span class="nv" style="color: #008080;">has</span> <span class="nv" style="color: #008080;">more</span> <span class="nv" style="color: #008080;">than</span> <span class="mi" style="color: #099;">65535</span> <span class="nv" style="color: #008080;">cigar</span> <span class="nv" style="color: #008080;">ops</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="nv" style="color: #008080;">Set</span> <span class="nv" style="color: #008080;">up</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">mkdir</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">p</span> <span class="nv" style="color: #008080;">$OUTDIR</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">Q</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DATDIR</span><span class="sr" style="color: #009926;">/long-cigar/</span><span class="nv" style="color: #008080;">query</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DATDIR</span><span class="sr" style="color: #009926;">/long-cigar/</span><span class="nb" style="color: #0086b3;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fasta</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="nv" style="color: #008080;">Test</span> <span class="nv" style="color: #008080;">m4</span> <span class="nv" style="color: #008080;">output</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">O</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OUTDIR</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">long</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">cigar</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">BLASR_EXE</span> <span class="nv" style="color: #008080;">$Q</span> <span class="nv" style="color: #008080;">$T</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">minMatch</span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">maxMatch</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">advanceHalf</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">advanceExactMatches</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">bestn</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">nproc</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">noSplitSubreads</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">out</span> <span class="nv" style="color: #008080;">$O</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">></span><span class="sr" style="color: #009926;">/dev/null</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">></span><span class="sr" style="color: #009926;">/dev/null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">echo</span> <span class="vg" style="color: #008080;">$?</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"> <span class="mi" style="color: #099;">0</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">grep</span> <span class="p">'</span><span class="s1" style="color: #d14;">CG:</span><span class="p">'</span> <span class="nv" style="color: #008080;">$O</span> <span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: #008080;">wc</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">l</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"> <span class="mi" style="color: #099;">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#490d9bbfafbadf3f3e9f14ae4eb510281bafe310"><strong>ctest/meson.build</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">@@ -32,6 +32,7 @@ blasr_fast_test_list = [</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> ['holeNumbers', 'INTERMEDIATE'],</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"># ['bug25328', 'SLOW'],</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"># ['pgc-big', 'SLOW'],</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"># ['long-cigar', 'SLOW'],</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">]</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">blasr_test_remotedir = '/pbi/dept/secondary/siv/testdata/BlasrTestData/ctest'</span>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#6cb9a3bc27980995c5a30f9048de8d8392d4665c"><strong>ctest/pgc-naive.t</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">@@ -53,6 +53,7 @@ Test bam output</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="nv" style="color: #008080;">O</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OUTDIR</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: #008080;">pgc</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">naive</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">bam</span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">BLASR_EXE</span> <span class="nv" style="color: #008080;">$Q</span> <span class="nv" style="color: #008080;">$T</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">bam</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">out</span> <span class="nv" style="color: #008080;">$O</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">bestn</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">--</span><span class="nv" style="color: #008080;">placeGapConsistently</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">echo</span> <span class="vg" style="color: #008080;">$?</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: #008080;">INFO</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"> <span class="nv" style="color: #008080;">WARNING</span><span class="p">,</span> <span class="nv" style="color: #008080;">BAM</span> <span class="nv" style="color: #008080;">output</span> <span class="nv" style="color: #008080;">without</span> <span class="nv" style="color: #008080;">PacBio</span> <span class="nv" style="color: #008080;">BAM</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nv" style="color: #008080;">DATASET</span> <span class="nv" style="color: #008080;">input</span> <span class="nv" style="color: #008080;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: #008080;">supported</span> <span class="nv" style="color: #008080;">by</span> <span class="nv" style="color: #008080;">PacBio</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: #008080;">INFO</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="perl"> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl"> <span class="nv" style="color: #008080;">$</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">SAMTOOLS_EXE</span> <span class="nv" style="color: #008080;">view</span> <span class="nv" style="color: #008080;">$O</span></span>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">blasr (5.3.3+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Afif removed himself from Uploaders (thanks for your work on this)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add myself to Uploaders</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 31 Jul 2019 14:55:41 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">blasr (5.3.2+dfsg-1.1) unstable; urgency=medium</span>
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2
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Non-maintainer upload.</span>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: blasr</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> python,</span>
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> meson,</span>
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8
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> pkg-config,</span>
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9
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libboost-dev,</span>
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<td class="diff-line-num old_line" 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">
10
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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libhdf5-dev,</span>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> zlib1g-dev,</span>
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12
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libpbseq-dev<span class="idiff left right"> (>= 0~20160912)</span>,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libpbseq-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libpbbam-dev (>= 0.18.0~),</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libpbdata-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libgtest-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libblasr-dev (>= 5.3.1+dfsg-2)</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/blasr</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/blasr.git</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/blasr</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">@@ -23,7 +24,7 @@ Package: blasr</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> libpbseq<span class="idiff left right"> (>= 0~20160912)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> libpbseq</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: mapping single-molecule sequencing reads</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> Basic local alignment with successive refinement (BLASR) is a method</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> for mapping single-molecule sequencing reads against a reference genome.</span>
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<li id="e58d34221dc60490c30dc9868da14030dd796433">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#e58d34221dc60490c30dc9868da14030dd796433"><strong>doc/EXAMPLES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Running BLASR</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"> Typing 'blasr -h' or 'blasr -help' on the command line will give you a</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"> list of options. At the least, provide <span class="idiff left right">a fasta, fastq, or bas.h5 file,</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"> <span class="idiff left right">and a genome</span>.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"> list of options. At the least, provide <span class="idiff left right">reads and a genome, where reads file format can be</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"> <span class="idiff left right">bam|dataset|fasta|fastq|bas.h5, and genome file format can be fasta|ReferenceSet</span>.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Some typical use cases</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">Align <span class="idiff left right">reads from reads.bas.h5 to ecoli_K12 genome, and output in S</span>AM format.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">Align <span class="idiff left right">subreads in movie.subreads.bam to ecoli_K12 genome, and output in B</span>AM format.</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">reads.bas.h5 ecoli_K12.fasta -s</span>am</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">movie.subreads.bam ecoli_K12.fasta --bam --out alignments.b</span>am</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">Same as above, but with soft clipping</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">Align subreads in movie.subreadset.xml to ecoli_K12 genome, and output in BAM format.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr movie.subreadset.xml ecoli_K12.fasta --bam --out alignments.bam</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">Align subreads in movie.subreadset.xml to ecoli_K12 genome ReferenceSet, and output in BAM format.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr movie.subreadset.xml ecoli_K12.referenceset.xml --bam --out alignments.bam</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="idiff left right">Align CCS reads in movie.consensusreadset.xml to ecoli_K12 genome, and output in BAM format.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="idiff left right">Use multiple threads</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> blasr movie.consensusreadset.xml ecoli_K12.fasta --bam --out alignments.bam</span></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">Use multiple threads, e.x., 16 threads</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr movie.subreads.bam ecoli_K12.fasta --nproc 16</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown">Include a larger minimal match, for faster but less sensitive alignments</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">reads.bas.h5 ecoli_K12.fasta -sam -clipping soft </span>-minMatch 15</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">movie.subreads.bam ecoli_K12.fasta -</span>-minMatch 15</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">Produce alignments in a pairwise human readable format</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">reads.bas.h5 </span> ecoli_K12.fasta -m 0</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr <span class="idiff left right">movie.subreads.bam</span> ecoli_K12.fasta -m 0</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown">Use a precomputed suffix array for faster startup</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sawriter ecoli_K12.fasta.sa ecoli_K12.fasta #First precompute the suffix array</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr movie.subreads.bam ecoli_K12.fasta --sa ecoli_K12.fasta.sa</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">Align RSII reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="idiff left right">Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> blasr reads.bas.h5 ecoli_K12.fasta --sam --out alignments.sam</span></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">Same as above, but with soft clipping</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;"> blasr reads.bas.h5 ecoli_K12.fasta --sam --clipping soft --out alignments.sam</span></span></pre>
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<li id="2e314a0e86c37cb69f20b01ef56cd17a325fd1d5">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#2e314a0e86c37cb69f20b01ef56cd17a325fd1d5"><strong>iblasr/MappingParameters.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +168,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useQVScore</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">scoreType</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">printVerboseHelp</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">printDiscussion</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">sdpBypassThreshold</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">computeAlignProbability</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">qvMatchWeight</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">@@ -346,7 +345,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"> <span class="n" style="color: #333;">guidedAlignBandSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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347
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="n" style="color: #333;">useQVScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">printVerboseHelp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">printDiscussion</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"> <span class="n" style="color: #333;">sdpBypassThreshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000000</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c"> <span class="n" style="color: #333;">scoreType</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c"> <span class="n" style="color: #333;">byAdapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -666,7 +664,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Only support two clipping methods: soft or subread.</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"> <span class="n" style="color: #333;">clipping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAMOutput</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">subread</span><span class="p">;</span></span>
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668
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Turn on fa fa -> <span class="idiff left right">b</span>am pipe</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Turn on fa fa -> <span class="idiff left right">s</span>am pipe</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if (queryFileType != FileType::PBBAM and queryFileType != FileType::PBDATASET and not enableHiddenPaths) {</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // bax|fasta|fastq -> bam paths are turned off by default</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">@@ -674,6 +672,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> std::exit(EXIT_FAILURE);</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ERROR, SAM output file must be specified."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</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">@@ -701,14 +700,14 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Only support two clipping methods: soft or subread.</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="c"> <span class="n" style="color: #333;">clipping</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAMOutput</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">subread</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Turn on fa fa -> bam pipe</span></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if (queryFileType != FileType::PBBAM and queryFileType != FileType::PBDATASET and not enableHiddenPaths) {</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> // bax|fasta|fastq -> bam paths are turned off by default</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> std::cout << "ERROR, could not output alignments in BAM unless input reads are in PacBio BAM or DATASET files." << std::endl;</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> std::exit(EXIT_FAILURE);</span></span>
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">queryFileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FileType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PBBAM</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">queryFileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FileType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PBDATASET</span> <span class="n" style="color: #333;">and</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">queryFileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FileType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HDFCCS</span> <span class="n" style="color: #333;">and</span> <span class="n" style="color: #333;">queryFileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FileType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HDFBase</span> <span class="n" style="color: #333;">and</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> <span class="n" style="color: #333;">queryFileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">FileType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HDFPulse</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// fasta|fastq -> bam paths are turned off by default</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"WARNING, BAM output without PacBio BAM or DATASET input is not "</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="c"> <span class="s" style="color: #d14;">"supported by PacBio."</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outFileName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="p">{</span></span>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ERROR, BAM output file must be specified."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>
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<li id="82db61cad929b7cbe4ae3a964d2f67365d4f4d20">
<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#82db61cad929b7cbe4ae3a964d2f67365d4f4d20"><strong>iblasr/RegisterBlasrOptions.h</strong></a>
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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">@@ -188,7 +188,7 @@ void RegisterBlasrOptions(CommandLineParser& clp, MappingParameters& params)</td>
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="n" style="color: #333;">clp</span><span class="p">.</span><span class="n" style="color: #333;">RegisterIntOption</span><span class="p">(</span><span class="s" style="color: #d14;">"-scoreType"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">scoreType</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">CommandLineParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NonNegativeInteger</span><span class="p">);</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">clp</span><span class="p">.</span><span class="n" style="color: #333;">RegisterFlagOption</span><span class="p">(</span><span class="s" style="color: #d14;">"h"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">printVerboseHelp</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">clp</span><span class="p">.</span><span class="n" style="color: #333;">RegisterFlagOption</span><span class="p">(</span><span class="s" style="color: #d14;">"-help"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">print<span class="idiff left right">Discussion</span></span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">clp</span><span class="p">.</span><span class="n" style="color: #333;">RegisterFlagOption</span><span class="p">(</span><span class="s" style="color: #d14;">"-help"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">print<span class="idiff left right">VerboseHelp</span></span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="n" style="color: #333;">clp</span><span class="p">.</span><span class="n" style="color: #333;">RegisterFloatOption</span><span class="p">(</span><span class="s" style="color: #d14;">"-accuracyPrior"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">readAccuracyPrior</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">CommandLineParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NonNegativeFloat</span><span class="p">);</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// holeNumberRangesStr is a string of comma-delimited hole number ranges, such as '1,2,3,10-15'.</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -225,7 +225,7 @@ void RegisterBlasrOptions(CommandLineParser& clp, MappingParameters& params)</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"><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="nf" style="color: #900; font-weight: 600;">BlasrHelp</span><span class="p">(</span><span class="n" style="color: #333;">MappingParameters</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">helpStream</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">o</span>stringstream</span> <span class="n" style="color: #333;">helpStream</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">helpStream</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Options for blasr "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "</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">@@ -629,13 +629,65 @@ const std::string BlasrHelp(MappingParameters& params)</td>
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629
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bioinformatics 2012, 13:238."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Please report any bugs to "</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'https://github.com/PacificBiosciences/blasr/issues'."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"DISCUSSION "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr is a read mapping program that maps reads to positions "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in a genome by clustering short exact matches between the read and"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" the genome, and scoring clusters using alignment. The matches are"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" generated by searching all suffixes of a read against the genome"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" using a suffix array. Global chaining methods are used to score "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" clusters of matches."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The only required inputs to blasr are a file of reads and a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reference genome. It is exremely useful to have read filtering"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" information, and mapping runtime may decrease substantially when a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" precomputed suffix array index on the reference sequence is"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" specified."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Although reads may be input in FASTA format, the recommended input is"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" PacBio BAM files because these contain quality value"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" information that is used in the alignment and produces higher quality"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" variant detection."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Although alignments can be output in various formats, the recommended "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" output format is PacBio BAM."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Support to bax.h5 and plx.h5 files will be DEPRECATED."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Support to region tables for h5 files will be DEPRECATED."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" When suffix array index of a genome is not specified, the suffix array is"</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" built before producing alignment. This may be prohibitively slow"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" when the genome is large (e.g. Human). It is best to precompute the"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" suffix array of a genome using the program sawriter, and then specify"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" the suffix array on the command line using -sa genome.fa.sa."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The optional parameters are roughly divided into three categories:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" control over anchoring, alignment scoring, and output. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The default anchoring parameters are optimal for small genomes and"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" samples with up to 5% divergence from the reference genome. The main"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" parameter governing speed and sensitivity is the -minMatch parameter."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For human genome alignments, a value of 11 or higher is recommended. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Several methods may be used to speed up alignments, at the expense of"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" possibly decreasing sensitivity. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Regions that are too repetitive may be ignored during mapping by"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" limiting the number of positions a read maps to with the"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -maxAnchorsPerPosition option. Values between 500 and 1000 are effective"</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in the human genome."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For small genomes such as bacterial genomes or BACs, the default parameters "</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" are sufficient for maximal sensitivity and good speed."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">helpStream</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="c"><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="nf" style="color: #900; font-weight: 600;">BlasrConciseHelp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">o</span>stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"blasr - a program to map reads to a genome"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" usage: blasr reads genome "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Run with -h for a list of commands "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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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">@@ -652,7 +704,7 @@ const std::string BlasrConciseHelp(void)</td>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="c"><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="nf" style="color: #900; font-weight: 600;">BlasrSummaryHelp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;"><span class="idiff left right">o</span>stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] "</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [option]</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Description (default_value)."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</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">@@ -674,93 +726,3 @@ const std::string BlasrSummaryHelp(void)</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ss</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="c"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="c"><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="nf" style="color: #900; font-weight: 600;">BlasrDiscussion</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"NAME"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr - Map SMRT Sequences to a reference genome."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SYNOPSIS"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.bam genome.fasta --bam --out out.bam"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.fasta genome.fasta "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.fasta genome.fasta --sa genome.fasta.sa"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.bax.h5 genome.fasta [--sa genome.fasta.sa] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.bax.h5 genome.fasta --sa genome.fasta.sa --maxScore 100 --minMatch "</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="c"> <span class="s" style="color: #d14;">"15 ... "</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr reads.bax.h5 genome.fasta --sa genome.fasta.sa --nproc 24 --out "</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="c"> <span class="s" style="color: #d14;">"alignment.out ... "</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"DESCRIPTION "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" blasr is a read mapping program that maps reads to positions "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in a genome by clustering short exact matches between the read and"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" the genome, and scoring clusters using alignment. The matches are"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" generated by searching all suffixes of a read against the genome"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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706
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" using a suffix array. Global chaining methods are used to score "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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707
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" clusters of matches."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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708
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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709
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The only required inputs to blasr are a file of reads and a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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710
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reference genome. It is exremely useful to have read filtering"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" information, and mapping runtime may decrease substantially when a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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712
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" precomputed suffix array index on the reference sequence is"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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713
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" specified."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Although reads may be input in FASTA format, the recommended input is"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" PacBio BAM files because these contain quality value"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" information that is used in the alignment and produces higher quality"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" variant detection."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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719
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Although alignments can be output in various formats, the recommended "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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720
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" output format is PacBio BAM."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Support to bax.h5 and plx.h5 files will be DEPRECATED."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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722
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Support to region tables for h5 files will be DEPRECATED."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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723
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " Read filtering information is contained in the .bax.h5 input files as" << std::endl</span></span>
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724
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " well as generated by other post-processing programs with analysis of" << std::endl</span></span>
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725
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " pulse files and read in from a separate .region.h5 file. The current" << std::endl</span></span>
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726
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " set of filters that are applied to reads are high quality region" << std::endl</span></span>
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727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " filtering, and adapter filtering. Regions outside high-quality" << std::endl</span></span>
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728
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " regions are ignored in mapping. Reads that contain regions annotated" << std::endl</span></span>
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729
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " as adapter are split into non-adapter (template) regions, and mapped" << std::endl</span></span>
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730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//<< " separately." << std::endl</span></span>
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731
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" When suffix array index of a genome is not specified, the suffix array is"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
</pre>
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733
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" built before producing alignment. This may be prohibitively slow"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
</pre>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" when the genome is large (e.g. Human). It is best to precompute the"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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735
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" suffix array of a genome using the program sawriter, and then specify"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" the suffix array on the command line using -sa genome.fa.sa."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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738
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<td class="diff-line-num new_line old" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The optional parameters are roughly divided into three categories:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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739
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<td class="diff-line-num new_line old" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" control over anchoring, alignment scoring, and output. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
741
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<td class="diff-line-num new_line old" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" The default anchoring parameters are optimal for small genomes and"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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742
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<pre style="margin: 0;">-<span id="LC742" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" samples with up to 5% divergence from the reference genome. The main"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
743
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<td class="diff-line-num new_line old" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" parameter governing speed and sensitivity is the -minMatch parameter."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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744
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For human genome alignments, a value of 11 or higher is recommended. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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745
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Several methods may be used to speed up alignments, at the expense of"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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746
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" possibly decreasing sensitivity. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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747
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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748
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " If the genome is highly repetitive or divergent from the read" << std::endl</span></span>
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749
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " sequences, the value of -maxExpand should be increased. This option" << std::endl</span></span>
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750
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<td class="diff-line-num new_line old" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " controls how much the search for anchors is expanded past a simple" << std::endl</span></span>
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751
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " greedy search. A value for -maxExpand of 1 is sufficent for" << std::endl</span></span>
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752
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " non-repetitive genomes, and values of -maxExpand greater than 5 are" << std::endl</span></span>
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753
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " not recommended." << std::endl</span></span>
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754
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// << " " << std::endl</span></span>
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755
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Regions that are too repetitive may be ignored during mapping by"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" limiting the number of positions a read maps to with the"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -maxAnchorsPerPosition option. Values between 500 and 1000 are effective"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in the human genome."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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760
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For small genomes such as bacterial genomes or BACs, the default parameters "</span></span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" are sufficient for maximal sensitivity and good speed."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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763
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="c"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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765
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ss</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">();</span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/blasr/compare/592ea642ec701da8f7e8407507a4a62f646e4270...869b0124b6fbcd97ca482f5daad79319485f584d#0cc1139e3347f573ae1feee5b73dbc8a8a21fcfa"><strong>meson.build</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">project(</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> 'blasr',</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> 'cpp',</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> version : '5.3.<span class="idiff left right">2</span>',</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> version : '5.3.<span class="idiff left right">3</span>',</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> default_options : [</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> 'buildtype=release',</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> 'warning_level=3',</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">@@ -77,13 +77,13 @@ blasr_config.set('BLASR_VERSION_MAJOR', blasr_major_version)</td>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">blasr_config.set('BLASR_VERSION_MINOR', blasr_minor_version)</span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">blasr_config.set('BLASR_VERSION_PATCH', blasr_patch_version)</span>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">configure_file(</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"><span class="idiff left right">blasr_BlasrVersion_h = </span>configure_file(</span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> input : 'BlasrVersion.h.in',</span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> output : 'BlasrVersion.h',</span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> configuration : blasr_config)</span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"># replace git commit id</span>
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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">blasr_<span class="idiff left right">git_commit_id</span> = vcs_tag(</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">blasr_<span class="idiff left right">BlasrGitHash_h</span> = vcs_tag(</span>
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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"> input : 'BlasrGitHash.h.in',</span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> output : 'BlasrGitHash.h',</span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> command : ['git', 'describe', '--always', '--dirty=*'],</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,16 +97,17 @@ subdir('extrautils')</td>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">subdir('utils')</span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">blasr_static_impl = static_library(</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> 'blasr_impl', [</span>
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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> blasr_sources,</span>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> blasr_git_commit_id],</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> 'blasr_impl',</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> blasr_sources,</span>
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<td class="diff-line-num 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">
103
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> install : false,</span>
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<td class="diff-line-num old_line" 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">
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> dependencies : blasr_deps,</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1'])</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">blasr_main = executable(</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"> 'blasr', files([</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> 'Blasr.cpp']),</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> 'blasr', [</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> blasr_BlasrGitHash_h,</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> blasr_BlasrVersion_h,</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> files('Blasr.cpp')],</span>
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110
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> install : true,</span>
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111
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"> dependencies : blasr_deps,</span>
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112
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext"> link_with : blasr_static_impl,</span>
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