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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/gmap">Debian Med / gmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/21441f4596e32a3e56bc98aa8b43a4ae65a21513">21441f45</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T07:56:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">document fix from Adrian bunk
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/9cc930cb562a3cf175f52076f86e6dc88ea1b0b0">9cc930cb</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T07:56:03+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop build-dep on dh-exec, not used any more
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/93e0adf9be429723f2e63536237a706929e4de59">93e0adf9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T08:08:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forwarded patches upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/605992535d3f44ccf28edb2eb266e103d6e30c31">60599253</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T08:15:12+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/5a9a58d3c47ac031dd4d156009f72f705475b655">5a9a58d3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T08:15:13+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021-02-22+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/28815453b5035af43de787ad8933e11113db83ef">28815453</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T08:15:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021-02-22+ds'
Update to upstream version '2021-02-22+ds'
with Debian dir b1228c746df333cc0cc4c4666150069459071a6b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/dd055d3614d3b1dc7e3b63394d3751f97e4edec0">dd055d36</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T09:31:55+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build on riscv64 as well
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc">34b6845f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-26T09:32:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a135a0121ee4d395bee62aa1facb3f3c790a51af">
debian/patches/cross
</a>
</li>
<li class="file-stats">
<a href="#cdc0f38341bcf0af07662569d0a0088b01f34fd3">
debian/patches/install-data-local
</a>
</li>
<li class="file-stats">
<a href="#5f772bf7d511ff5b65692445dc90e2d809e8ca10">
debian/patches/only-do-cpuid-on-amd64-i386.patch
</a>
</li>
<li class="file-stats">
<a href="#9fd77014d4c25b9aab7109c2e97ddfe7a415d292">
debian/patches/remove_getopt_code_copy.patch
</a>
</li>
<li class="file-stats">
<a href="#959dc4d7bc7cbf46f686ae1a0069076131926bcc">
src/samprint.c
</a>
</li>
<li class="file-stats">
<a href="#2d331dd15dccff926559b191048c3a7d2d3a5fae">
src/stage3hr.c
</a>
</li>
<li class="file-stats">
<a href="#aeb285890115a453e6448fd7de6fc67bf8daf3a4">
src/substring.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">2021-02-23 twu</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang=""> * VERSION, index.html: Updated version number</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="">2021-02-22 twu</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang=""> * stage3hr.c: In removing overlaps, handling the case where hitlist or</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang=""> hitpairlist is NULL. Using low and high instead of genomicstart and</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang=""> genomicend to compute insertlength</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang=""> * substring.c: Added commented code</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang=""> * samprint.c: Using pairtype for concordant pairs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="">2021-02-14 twu</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang=""> * index.html: Updated for latest version</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2021-02-12</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2021-02-22</span></pre>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gmap (2021-02-22+ds-1) unstable; urgency=high</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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream release: "Fixed a fatal bug in GSNAP involving reads aligning</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> to the beginning of the genome"</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debian/rules: fix from Adrian Bunk to fix the i386 build</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Drop build-dep on dh-exec, not used any more</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Forwarded patches upstream</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Build on riscv64 as well</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"> -- Michael R. Crusoe <crusoe@debian.org> Fri, 26 Feb 2021 08:15:33 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">gmap (2021-02-12+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,6 @@ Uploaders: Shaun Jackman <sjackman@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> dh-exec,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> help2man,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +17,7 @@ Homepage: http://research-pub.gene.com/gmap</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: gmap</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Architecture: amd64 arm64 armel armhf i386 mips64el mipsel ppc64el</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Architecture: amd64 arm64 armel armhf i386 mips64el mipsel ppc64el<span class="idiff left right"> riscv64</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">#not s390x</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${perl:Depends},</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#a135a0121ee4d395bee62aa1facb3f3c790a51af"><strong>debian/patches/cross</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Helmut Grohne <helmut@subdivi.de></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: Work towards more cross-building support</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Origin: vendor, https://bugs.debian.org/cgi-bin/bugreport.cgi?att=1;bug=980484;filename=cross.patch;msg=5</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: yes</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> email sent to twu@gene.com on 2021-02-26</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gmap-2020-12-17+ds.orig/config/builtin-popcount.m4</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gmap-2020-12-17+ds/config/builtin-popcount.m4</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -33,29 +33,41 @@</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#cdc0f38341bcf0af07662569d0a0088b01f34fd3"><strong>debian/patches/install-data-local</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Install data local</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Forwarded: yes</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> email sent to twu@gene.com on 2021-02-26</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Index: gmap/Makefile.am</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#5f772bf7d511ff5b65692445dc90e2d809e8ca10"><strong>debian/patches/only-do-cpuid-on-amd64-i386.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@ Description: Only do CPUID on amd64 and i386</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This fixes a FTBFS on armhf and arm64.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Author: Graham Inggs <ginggs@ubuntu.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2016-07-24</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: yes</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> email sent to twu@gene.com on 2021-02-26</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gmap.orig/src/cpuid.c</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gmap/src/cpuid.c</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span></span>
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<li id="9fd77014d4c25b9aab7109c2e97ddfe7a415d292">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#9fd77014d4c25b9aab7109c2e97ddfe7a415d292"><strong>debian/patches/remove_getopt_code_copy.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Sat, 11 Apr 2020 18:03:49 +0200</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: getline belongs to libc - no need to have a copy here</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: yes</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> email sent to twu@gene.com on 2021-02-26</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -196,7 +196,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#959dc4d7bc7cbf46f686ae1a0069076131926bcc"><strong>src/samprint.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: samprint.c 223<span class="idiff left">774</span> 202<span class="idiff right">0-12-14 19:16:04</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: samprint.c 223<span class="idiff left">817</span> 202<span class="idiff right">1-02-23 07:37:42</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -1351,7 +1351,8 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev, Stage3pai</td>
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="c"> <span class="n" style="color: #333;">Hittype_T</span> <span class="n" style="color: #333;">hittype</span><span class="p">;</span></span>
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="c"> <span class="n" style="color: #333;">Substring_T</span> <span class="n" style="color: #333;">donor</span><span class="p">,</span> <span class="n" style="color: #333;">acceptor</span><span class="p">;</span></span>
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1353
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="c"></span>
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1354
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<pre style="margin: 0;">-<span id="LC1354" class="line" lang="c"> <span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Entered SAM_print of hit %p with hittype %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">this</span><span class="p">,</span><span class="n" style="color: #333;">Stage3end_hittype_string</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)));</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="c"> <span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Entered SAM_print of hit %p with hittype %s and abbrev %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="p">,</span><span class="n" style="color: #333;">Stage3end_hittype_string</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">),</span><span class="n" style="color: #333;">abbrev</span><span class="p">));</span></span>
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="c"></span>
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1356
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1357
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Test for nomapping was chrpos == 0, but we can actually align to chrpos 0 */</span></span>
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1357
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1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Also, can use this test here because --quiet-if-excessive cases go directly to SAM_print_nomapping */</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">@@ -1506,15 +1507,38 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f</td>
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1506
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1507
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<pre style="margin: 0;"> <span id="LC1507" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">clip_overlap_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">merge_overlap_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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1507
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1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="c"> <span class="n" style="color: #333;">clipdir</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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1508
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="c"> <span class="n" style="color: #333;">hardclip5_low</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hardclip5_high</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hardclip3_low</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hardclip3_high</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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1509
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<pre style="margin: 0;">-<span id="LC1509" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CU</span><span class="p">);</span></span>
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1510
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<pre style="margin: 0;">-<span id="LC1510" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_CONCORDANT_UNIQ</span><span class="p">;</span></span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_determine_pairtype</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_SCRAMBLE</span><span class="p">)</span> <span class="p">{</span></span>
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1511
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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PS</span><span class="p">);</span></span>
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1512
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<pre style="margin: 0;">+<span id="LC1512" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_SCR</span><span class="p">;</span></span>
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1513
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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_INVERSION</span><span class="p">)</span> <span class="p">{</span></span>
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1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PI</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_INV</span><span class="p">;</span></span>
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1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_TOOLONG</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PL</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_LONG</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CU</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_CONCORDANT_UNIQ</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="c"> <span class="p">}</span></span>
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1511
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<td class="new_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="c"> </span>
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<td class="old_line diff-line-num" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
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<td class="new_line diff-line-num" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1513
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<td class="new_line diff-line-num" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<pre style="margin: 0;"> <span id="LC1525" class="line" lang="c"> <span class="n" style="color: #333;">clipdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_overlap</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hardclip5_low</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hardclip5_high</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hardclip3_low</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hardclip3_high</span><span class="p">,</span><span class="n" style="color: #333;">stage3pair</span><span class="p">);</span></span>
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1514
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<td class="new_line diff-line-num" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="c"> <span class="n" style="color: #333;">debug3</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"clipdir %d with hardclip5 = %d..%d, hardclip3 = %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<td class="new_line diff-line-num" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<pre style="margin: 0;"> <span id="LC1527" class="line" lang="c"> <span class="n" style="color: #333;">clipdir</span><span class="p">,</span><span class="n" style="color: #333;">hardclip5_low</span><span class="p">,</span><span class="n" style="color: #333;">hardclip5_high</span><span class="p">,</span><span class="n" style="color: #333;">hardclip3_low</span><span class="p">,</span><span class="n" style="color: #333;">hardclip3_high</span><span class="p">));</span></span>
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1516
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<td class="new_line diff-line-num" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CU</span><span class="p">);</span></span>
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1517
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<td class="new_line diff-line-num old" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1517" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_CONCORDANT_UNIQ</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_determine_pairtype</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_SCRAMBLE</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PS</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_SCR</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_INVERSION</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PI</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_INV</span><span class="p">;</span></span>
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1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_TOOLONG</span><span class="p">)</span> <span class="p">{</span></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PL</span><span class="p">);</span></span>
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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_UNIQ_LONG</span><span class="p">;</span></span>
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1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CU</span><span class="p">);</span></span>
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1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_CONCORDANT_UNIQ</span><span class="p">;</span></span>
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1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="c"> <span class="p">}</span></span>
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="c"> <span class="p">}</span></span>
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="c"> <span class="p">}</span></span>
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1544
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1706,7 +1730,21 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f</td>
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="c"></span>
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1707
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1708
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1732
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<pre style="margin: 0;"> <span id="LC1732" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */</span></span>
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<pre style="margin: 0;">-<span id="LC1709" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CM</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="c"> <span class="n" style="color: #333;">stage3pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stage3pairarray</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Stage3pair_determine_pairtype</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_SCRAMBLE</span><span class="p">)</span> <span class="p">{</span></span>
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1735
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PM</span><span class="p">);</span></span>
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1736
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_MULT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1737" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_INVERSION</span><span class="p">)</span> <span class="p">{</span></span>
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1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PM</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_MULT</span><span class="p">;</span></span>
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1740
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PAIRED_TOOLONG</span><span class="p">)</span> <span class="p">{</span></span>
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1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_PM</span><span class="p">);</span></span>
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1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_PAIRED_MULT</span><span class="p">;</span></span>
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1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="c"> <span class="n" style="color: #333;">Filestring_set_split_output</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">OUTPUT_CM</span><span class="p">);</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="c"> <span class="n" style="color: #333;">abbrev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ABBREV_CONCORDANT_MULT</span><span class="p">;</span></span>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="c"> <span class="p">}</span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="c"></span>
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1710
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1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">pathnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">npaths_primary</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">npaths_altloc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pathnum</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">maxpaths_report</span><span class="p">;</span> <span class="n" style="color: #333;">pathnum</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1749
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<pre style="margin: 0;"> <span id="LC1749" class="line" lang="c"></span>
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1712
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1750
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="c"> <span class="n" style="color: #333;">stage3pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stage3pairarray</span><span class="p">[</span><span class="n" style="color: #333;">pathnum</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1737,7 +1775,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f</td>
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1737
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1775
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<pre style="margin: 0;"> <span id="LC1775" class="line" lang="c"></span>
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1776
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<pre style="margin: 0;"> <span id="LC1776" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">merge_overlap_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">clipdir</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1739
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1777
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<pre style="margin: 0;"> <span id="LC1777" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print first end */</span></span>
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1740
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<pre style="margin: 0;">-<span id="LC1740" class="line" lang="c"> <span class="n" style="color: #333;">SAM_print</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">ABBREV_CONCORDANT_MULT</span></span><span class="p">,</span><span class="n" style="color: #333;">stage3pair</span><span class="p">,</span></span>
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1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="c"> <span class="n" style="color: #333;">SAM_print</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_1</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">abbrev</span></span><span class="p">,</span><span class="n" style="color: #333;">stage3pair</span><span class="p">,</span></span>
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1741
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1779
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<pre style="margin: 0;"> <span id="LC1779" class="line" lang="c"> <span class="n" style="color: #333;">hit5</span><span class="p">,</span><span class="n" style="color: #333;">querylength5</span><span class="p">,</span><span class="n" style="color: #333;">acc1</span><span class="p">,</span><span class="n" style="color: #333;">acc2</span><span class="p">,</span><span class="n" style="color: #333;">pathnum</span><span class="p">,</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span></span>
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1742
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1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_absmq_score</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">),</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="n" style="color: #333;">second_absmq</span><span class="p">,</span></span>
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1743
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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_mapq_score</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">),</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1749,7 +1787,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f</td>
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1749
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1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="c"> <span class="n" style="color: #333;">quality_shift</span><span class="p">,</span><span class="n" style="color: #333;">sam_read_group_id</span><span class="p">,</span><span class="n" style="color: #333;">invert_first_p</span><span class="p">,</span><span class="n" style="color: #333;">invert_second_p</span><span class="p">);</span></span>
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1750
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1788
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<pre style="margin: 0;"> <span id="LC1788" class="line" lang="c"></span>
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1751
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1789
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<pre style="margin: 0;"> <span id="LC1789" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print second end */</span></span>
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1752
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<pre style="margin: 0;">-<span id="LC1752" class="line" lang="c"> <span class="n" style="color: #333;">SAM_print</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">ABBREV_CONCORDANT_MULT</span></span><span class="p">,</span><span class="n" style="color: #333;">stage3pair</span><span class="p">,</span></span>
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1790
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<pre style="margin: 0;">+<span id="LC1790" class="line" lang="c"> <span class="n" style="color: #333;">SAM_print</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;">fp_failedinput_2</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">abbrev</span></span><span class="p">,</span><span class="n" style="color: #333;">stage3pair</span><span class="p">,</span></span>
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1753
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1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="c"> <span class="n" style="color: #333;">hit3</span><span class="p">,</span><span class="n" style="color: #333;">querylength3</span><span class="p">,</span><span class="n" style="color: #333;">acc1</span><span class="p">,</span><span class="n" style="color: #333;">acc2</span><span class="p">,</span><span class="n" style="color: #333;">pathnum</span><span class="p">,</span><span class="n" style="color: #333;">npaths_primary</span><span class="p">,</span><span class="n" style="color: #333;">npaths_altloc</span><span class="p">,</span></span>
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1754
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1792
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<pre style="margin: 0;"> <span id="LC1792" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_absmq_score</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">),</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="n" style="color: #333;">second_absmq</span><span class="p">,</span></span>
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1755
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1793
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<pre style="margin: 0;"> <span id="LC1793" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_mapq_score</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">),</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1827" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1789,7 +1827,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f</td>
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1789
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1827
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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="c"> <span class="n" style="color: #333;">Stage3pair_absmq_score</span><span class="p">(</span><span class="n" style="color: #333;">stage3pair</span><span class="p">),</span><span class="n" style="color: #333;">first_absmq</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*invertp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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1790
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<td class="new_line diff-line-num" data-linenumber="1828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1828
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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*invert_mate_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*supplementaryp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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1791
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1829
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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="c"></span>
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1792
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<pre style="margin: 0;">-<span id="LC1792" class="line" lang="c"> <span class="n" style="color: #333;">Simplepair_overlap_print_sam</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">ABBREV_CONCORDANT_MULT</span></span><span class="p">,</span><span class="n" style="color: #333;">pairarray</span><span class="p">,</span><span class="n" style="color: #333;">npairs</span><span class="p">,</span></span>
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1830
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<pre style="margin: 0;">+<span id="LC1830" class="line" lang="c"> <span class="n" style="color: #333;">Simplepair_overlap_print_sam</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left right">abbrev</span></span><span class="p">,</span><span class="n" style="color: #333;">pairarray</span><span class="p">,</span><span class="n" style="color: #333;">npairs</span><span class="p">,</span></span>
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1793
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1831
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<pre style="margin: 0;"> <span id="LC1831" class="line" lang="c"> <span class="n" style="color: #333;">acc1</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*acc2*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">Stage3end_chrnum</span><span class="p">(</span><span class="n" style="color: #333;">hit5</span><span class="p">),</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span></span>
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1794
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1832
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<pre style="margin: 0;"> <span id="LC1832" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*queryseq_ptr*/</span><span class="n" style="color: #333;">queryseq_merged</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*quality_string*/</span><span class="n" style="color: #333;">quality_merged</span><span class="p">,</span></span>
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1795
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1833
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<pre style="margin: 0;"> <span id="LC1833" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*hardclip_low*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*hardclip_high*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*querylength*/</span><span class="n" style="color: #333;">querylength_merged</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#2d331dd15dccff926559b191048c3a7d2d3a5fae"><strong>src/stage3hr.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 2238<span class="idiff left">08</span> 2021-02-<span class="idiff">1</span>3 <span class="idiff right">18:47:25</span>Z twu $";</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 2238<span class="idiff left">19</span> 2021-02-<span class="idiff">2</span>3 <span class="idiff right">07:39:23</span>Z twu $";</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="">#ifdef HAVE_CONFIG_H</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="">#include "config.h"</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="">#endif</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6537" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6537,7 +6537,7 @@ pair_insert_length (int *pair_relationship, Stage3end_T hit5, Stage3end_T hit3)</td>
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6537
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6537
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<pre style="margin: 0;"> <span id="LC6537" class="line" lang=""></span>
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6538
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6538
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<pre style="margin: 0;"> <span id="LC6538" class="line" lang=""> /* No overlap found between any combination of substrings */</span>
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6539
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6539
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<pre style="margin: 0;"> <span id="LC6539" class="line" lang=""> if (hit5->plusp == true) {</span>
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6540
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<pre style="margin: 0;">-<span id="LC6540" class="line" lang=""> if (hit5-><span class="idiff left right">genomicend > hit3->genomicstart</span> + hit5->querylength + hit3->querylength) {</span>
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6540
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<pre style="margin: 0;">+<span id="LC6540" class="line" lang=""> if (hit5-><span class="idiff left right">high > hit3->low</span> + hit5->querylength + hit3->querylength) {</span>
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6541
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6541
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<pre style="margin: 0;"> <span id="LC6541" class="line" lang=""> debug10(printf("pair_insert_length: no overlap found, and %u - %u + %d + %d < 0, so returning 0\n",</span>
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6542
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6542
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<pre style="margin: 0;"> <span id="LC6542" class="line" lang=""> hit3->genomicstart - hit3->chroffset,hit5->genomicend - hit5->chroffset,</span>
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6543
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6543
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<pre style="margin: 0;"> <span id="LC6543" class="line" lang=""> hit5->querylength,hit3->querylength));</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6549" style="width: 35px; color: rgba(0,0,0,0.3); 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="6549" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -6549,10 +6549,10 @@ pair_insert_length (int *pair_relationship, Stage3end_T hit5, Stage3end_T hit3)</td>
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6549
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6549
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<pre style="margin: 0;"> <span id="LC6549" class="line" lang=""> hit5->querylength,hit3->querylength));</span>
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6550
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6550
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<pre style="margin: 0;"> <span id="LC6550" class="line" lang=""> }</span>
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6551
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6551
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<pre style="margin: 0;"> <span id="LC6551" class="line" lang=""> *pair_relationship = +1;</span>
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6552
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<pre style="margin: 0;">-<span id="LC6552" class="line" lang=""> return hit3-><span class="idiff left right">genomicstart - hit5->genomicend</span> + hit5->querylength + hit3->querylength;</span>
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6552
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<pre style="margin: 0;">+<span id="LC6552" class="line" lang=""> return hit3-><span class="idiff left right">low - hit5->high</span> + hit5->querylength + hit3->querylength;</span>
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6553
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6553
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<pre style="margin: 0;"> <span id="LC6553" class="line" lang=""></span>
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6554
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6554
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<pre style="margin: 0;"> <span id="LC6554" class="line" lang=""> } else {</span>
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6555
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<pre style="margin: 0;">-<span id="LC6555" class="line" lang=""> if (hit3-><span class="idiff left right">genomicstart > hit5->genomicend</span> + hit5->querylength + hit3->querylength) {</span>
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6555
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<pre style="margin: 0;">+<span id="LC6555" class="line" lang=""> if (hit3-><span class="idiff left right">high > hit5->low</span> + hit5->querylength + hit3->querylength) {</span>
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6556
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6556
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<pre style="margin: 0;"> <span id="LC6556" class="line" lang=""> debug10(printf("pair_insert_length: no overlap found, and %u - %u + %d + %d < 0, so returning 0\n",</span>
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6557
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6557
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<pre style="margin: 0;"> <span id="LC6557" class="line" lang=""> hit5->genomicend - hit5->chroffset,hit3->genomicstart - hit3->chroffset,</span>
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6558
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6558
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<pre style="margin: 0;"> <span id="LC6558" class="line" lang=""> hit5->querylength,hit3->querylength));</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">@@ -6563,7 +6563,7 @@ pair_insert_length (int *pair_relationship, Stage3end_T hit5, Stage3end_T hit3)</td>
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6563
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6563
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<pre style="margin: 0;"> <span id="LC6563" class="line" lang=""> hit5->genomicend - hit5->chroffset,hit3->genomicstart - hit3->chroffset,</span>
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6564
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6564
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<pre style="margin: 0;"> <span id="LC6564" class="line" lang=""> hit5->querylength,hit3->querylength));</span>
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6565
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6565
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<pre style="margin: 0;"> <span id="LC6565" class="line" lang=""> *pair_relationship = -1;</span>
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6566
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<pre style="margin: 0;">-<span id="LC6566" class="line" lang=""> return hit5-><span class="idiff left right">genomicend - hit3->genomicstart</span> + hit5->querylength + hit3->querylength;</span>
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6566
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<pre style="margin: 0;">+<span id="LC6566" class="line" lang=""> return hit5-><span class="idiff left right">low - hit3->high</span> + hit5->querylength + hit3->querylength;</span>
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6567
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6567
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<pre style="margin: 0;"> <span id="LC6567" class="line" lang=""> }</span>
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6568
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6568
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<pre style="margin: 0;"> <span id="LC6568" class="line" lang=""> }</span>
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6569
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6569
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<pre style="margin: 0;"> <span id="LC6569" class="line" lang="">}</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7057" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -7057,9 +7057,11 @@ Stage3end_optimal_score_final_old (bool *eliminatedp, List_T hitlist, Hitlistpoo</td>
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7057
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7057
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<pre style="margin: 0;"> <span id="LC7057" class="line" lang=""> }</span>
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7058
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7058
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<pre style="margin: 0;"> <span id="LC7058" class="line" lang=""> }</span>
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7059
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7059
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<pre style="margin: 0;"> <span id="LC7059" class="line" lang=""> Hitlist_free(&hitlist);</span>
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7060
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<pre style="margin: 0;">-<span id="LC7060" class="line" lang=""> hitlist = optimal;</span>
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7061
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<pre style="margin: 0;">-<span id="LC7061" class="line" lang=""> optimal = (List_T) NULL;</span>
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7062
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<pre style="margin: 0;">-<span id="LC7062" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC7060" class="line" lang=""> if ((hitlist = optimal) == NULL) {</span>
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7061
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<pre style="margin: 0;">+<span id="LC7061" class="line" lang=""> return (List_T) NULL;</span>
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<pre style="margin: 0;">+<span id="LC7062" class="line" lang=""> } else {</span>
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<pre style="margin: 0;">+<span id="LC7063" class="line" lang=""> optimal = (List_T) NULL;</span>
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7064
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<pre style="margin: 0;">+<span id="LC7064" class="line" lang=""> }</span>
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7065
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<pre style="margin: 0;"> <span id="LC7065" class="line" lang=""></span>
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7064
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7066
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<pre style="margin: 0;"> <span id="LC7066" class="line" lang=""> /* Prune based on ref_nmatches_plus_spliced_trims (to get the splice ends) */</span>
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7065
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7067
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<pre style="margin: 0;"> <span id="LC7067" class="line" lang=""> max_nmatches = 0;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7133" style="width: 35px; color: rgba(0,0,0,0.3); 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="7135" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -7133,8 +7135,11 @@ Stage3end_optimal_score_final_old (bool *eliminatedp, List_T hitlist, Hitlistpoo</td>
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7133
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7135
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<pre style="margin: 0;"> <span id="LC7135" class="line" lang=""> }</span>
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7134
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7136
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<pre style="margin: 0;"> <span id="LC7136" class="line" lang=""> }</span>
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7135
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7137
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<pre style="margin: 0;"> <span id="LC7137" class="line" lang=""> Hitlist_free(&hitlist);</span>
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7136
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<pre style="margin: 0;">-<span id="LC7136" class="line" lang=""> hitlist = optimal;</span>
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7137
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<pre style="margin: 0;">-<span id="LC7137" class="line" lang=""> optimal = (List_T) NULL;</span>
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7138
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<pre style="margin: 0;">+<span id="LC7138" class="line" lang=""> if ((hitlist = optimal) == NULL) {</span>
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<td class="new_line diff-line-num new" data-linenumber="7139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7139
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<pre style="margin: 0;">+<span id="LC7139" class="line" lang=""> return (List_T) NULL;</span>
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<td class="new_line diff-line-num new" data-linenumber="7140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7140
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<pre style="margin: 0;">+<span id="LC7140" class="line" lang=""> } else {</span>
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<td class="new_line diff-line-num new" data-linenumber="7141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7141
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<pre style="margin: 0;">+<span id="LC7141" class="line" lang=""> optimal = (List_T) NULL;</span>
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7142
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<pre style="margin: 0;">+<span id="LC7142" class="line" lang=""> }</span>
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7138
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7143
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<pre style="margin: 0;"> <span id="LC7143" class="line" lang=""></span>
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7139
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7144
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<pre style="margin: 0;"> <span id="LC7144" class="line" lang=""></span>
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7140
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7145
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<pre style="margin: 0;"> <span id="LC7145" class="line" lang=""> /* Eliminate within loci (1): refalt_nmatches_to_trims only */</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7195" style="width: 35px; color: rgba(0,0,0,0.3); 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="7200" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -7195,9 +7200,12 @@ Stage3end_optimal_score_final_old (bool *eliminatedp, List_T hitlist, Hitlistpoo</td>
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7195
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7200
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<pre style="margin: 0;"> <span id="LC7200" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7196
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<td class="new_line diff-line-num" data-linenumber="7201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7201
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7201" class="line" lang=""> FREE(hits);</span>
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7197
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<td class="new_line diff-line-num" data-linenumber="7202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7202
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<pre style="margin: 0;"> <span id="LC7202" class="line" lang=""> FREE(eliminate);</span>
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7198
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<pre style="margin: 0;">-<span id="LC7198" class="line" lang=""> hitlist = optimal;</span>
</pre>
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7199
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<pre style="margin: 0;">-<span id="LC7199" class="line" lang=""> optimal = (List_T) NULL;</span>
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7200
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<pre style="margin: 0;">-<span id="LC7200" class="line" lang=""></span>
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7203
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<pre style="margin: 0;">+<span id="LC7203" class="line" lang=""> if ((hitlist = optimal) == NULL) {</span>
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7204
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<pre style="margin: 0;">+<span id="LC7204" class="line" lang=""> return (List_T) NULL;</span>
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7205
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<pre style="margin: 0;">+<span id="LC7205" class="line" lang=""> } else {</span>
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7206
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<pre style="margin: 0;">+<span id="LC7206" class="line" lang=""> optimal = (List_T) NULL;</span>
</pre>
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7207
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<pre style="margin: 0;">+<span id="LC7207" class="line" lang=""> }</span>
</pre>
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7208
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<pre style="margin: 0;">+<span id="LC7208" class="line" lang=""> </span>
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7201
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7209
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<pre style="margin: 0;"> <span id="LC7209" class="line" lang=""></span>
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7202
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<td class="new_line diff-line-num" data-linenumber="7210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7210
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<pre style="margin: 0;"> <span id="LC7210" class="line" lang=""> /* Eliminate within loci (2): nsegments and splice score */</span>
</pre>
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7203
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<td class="new_line diff-line-num" data-linenumber="7211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7211
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<pre style="margin: 0;"> <span id="LC7211" class="line" lang=""> keptp = false;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9426" style="width: 35px; color: rgba(0,0,0,0.3); 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="9434" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9426,7 +9434,12 @@ Stage3end_remove_overlaps (List_T hitlist, Hitlistpool_T hitlistpool, int queryl</td>
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9426
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<td class="new_line diff-line-num" data-linenumber="9434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9434
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<pre style="margin: 0;"> <span id="LC9434" class="line" lang=""> /* Prune based on nmatches adjusted by score to get a tradeoff between matches and parsimony */</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9427
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<td class="new_line diff-line-num" data-linenumber="9435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9435
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<pre style="margin: 0;"> <span id="LC9435" class="line" lang=""> /* Same as step 1 of Stage3pair_optimal_score_final */</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9428
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<td class="new_line diff-line-num" data-linenumber="9436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9436
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<pre style="margin: 0;"> <span id="LC9436" class="line" lang=""> debug8(printf(" Step 3. Maximize nmatches adjusted by score (with slop)\n"));</span>
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<td class="old_line diff-line-num old" data-linenumber="9429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9429
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<td class="new_line diff-line-num old" data-linenumber="9437" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC9429" class="line" lang=""> optimal = (List_T) NULL;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9430" style="width: 35px; color: rgba(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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9437
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<pre style="margin: 0;">+<span id="LC9437" class="line" lang=""> if (hitlist == NULL) {</span>
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<td class="old_line diff-line-num new" data-linenumber="9430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="9438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9438
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<pre style="margin: 0;">+<span id="LC9438" class="line" lang=""> return (List_T) NULL;</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="9430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="9439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9439
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<pre style="margin: 0;">+<span id="LC9439" class="line" lang=""> } else {</span>
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<td class="new_line diff-line-num new" data-linenumber="9440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9440
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<pre style="margin: 0;">+<span id="LC9440" class="line" lang=""> optimal = (List_T) NULL;</span>
</pre>
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9441
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<pre style="margin: 0;">+<span id="LC9441" class="line" lang=""> }</span>
</pre>
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9442
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<pre style="margin: 0;">+<span id="LC9442" class="line" lang=""> </span>
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9430
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9443
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<pre style="margin: 0;"> <span id="LC9443" class="line" lang=""></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9431
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9444
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<pre style="margin: 0;"> <span id="LC9444" class="line" lang=""> keptp = false;</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9432
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<td class="new_line diff-line-num" data-linenumber="9445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9445
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9445" class="line" lang=""> hits = (T *) List_to_array_n(&n,hitlist);</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9493" style="width: 35px; color: rgba(0,0,0,0.3); 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="9506" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -9493,13 +9506,16 @@ Stage3end_remove_overlaps (List_T hitlist, Hitlistpool_T hitlistpool, int queryl</td>
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9493
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9506
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<pre style="margin: 0;"> <span id="LC9506" class="line" lang=""> }</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9494
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<td class="new_line diff-line-num" data-linenumber="9507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9507
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<pre style="margin: 0;"> <span id="LC9507" class="line" lang=""> FREE(hits);</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="9495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9495
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<td class="new_line diff-line-num" data-linenumber="9508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9508
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9508" class="line" lang=""> FREE(eliminate);</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="9496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9496
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<td class="new_line diff-line-num old" data-linenumber="9509" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC9496" class="line" lang=""> hitlist = optimal;</span>
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<td class="old_line diff-line-num old" data-linenumber="9497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9497
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<td class="new_line diff-line-num old" data-linenumber="9509" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC9497" class="line" lang=""></span>
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<td class="new_line diff-line-num new" data-linenumber="9509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9509
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<pre style="margin: 0;">+<span id="LC9509" class="line" lang=""> if ((hitlist = optimal) == NULL) {</span>
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<td class="new_line diff-line-num new" data-linenumber="9510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9510
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<pre style="margin: 0;">+<span id="LC9510" class="line" lang=""> return (List_T) NULL;</span>
</pre>
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9511
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<pre style="margin: 0;">+<span id="LC9511" class="line" lang=""> } else {</span>
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9512
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<pre style="margin: 0;">+<span id="LC9512" class="line" lang=""> optimal = (List_T) NULL;</span>
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9513
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<pre style="margin: 0;">+<span id="LC9513" class="line" lang=""> }</span>
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9514
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<pre style="margin: 0;">+<span id="LC9514" class="line" lang=""> </span>
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9498
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9515
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<pre style="margin: 0;"> <span id="LC9515" class="line" lang=""></span>
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9499
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9516
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<pre style="margin: 0;"> <span id="LC9516" class="line" lang=""> /* Eliminate within loci: minimize nsegments and maximize splice score */</span>
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9500
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9517
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<pre style="margin: 0;"> <span id="LC9517" class="line" lang=""> /* Since we have achieved same number of matches, we should minimize nsegments to achieve parsimony */</span>
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9501
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9518
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<pre style="margin: 0;"> <span id="LC9518" class="line" lang=""> debug4(printf(" Step 4. Minimize nsegments and splice score\n"));</span>
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9502
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<pre style="margin: 0;">-<span id="LC9502" class="line" lang=""> optimal = (List_T) NULL;</span>
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9503
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9519
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<pre style="margin: 0;"> <span id="LC9519" class="line" lang=""></span>
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9504
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9520
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<pre style="margin: 0;"> <span id="LC9520" class="line" lang=""> keptp = false;</span>
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9505
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9521
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<pre style="margin: 0;"> <span id="LC9521" class="line" lang=""> hits = (T *) List_to_array_n(&n,hitlist);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11469" style="width: 35px; color: rgba(0,0,0,0.3); 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="11485" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -11469,11 +11485,11 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11469
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11485
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<pre style="margin: 0;"> <span id="LC11485" class="line" lang=""> /* or 3-end..start and 5-start..end */</span>
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11470
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11486
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<pre style="margin: 0;"> <span id="LC11486" class="line" lang=""></span>
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11471
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11487
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<pre style="margin: 0;"> <span id="LC11487" class="line" lang=""> new->pair_relationship = 0;</span>
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11472
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<pre style="margin: 0;">-<span id="LC11472" class="line" lang=""> if (hit5-><span class="idiff left right">genomicend < hit3->genomicend</span>) {</span>
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11473
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<pre style="margin: 0;">-<span id="LC11473" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">genomicend - hit5->genomicend</span>) + querylength5 + querylength3;</span>
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11488
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<pre style="margin: 0;">+<span id="LC11488" class="line" lang=""> if (hit5-><span class="idiff left right">high < hit3->low</span>) {</span>
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11489
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<pre style="margin: 0;">+<span id="LC11489" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">low - hit5->high</span>) + querylength5 + querylength3;</span>
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11474
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11490
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<pre style="margin: 0;"> <span id="LC11490" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
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11475
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<pre style="margin: 0;">-<span id="LC11475" class="line" lang=""> } else if (hit3-><span class="idiff left right">genomicstart < hit5->genomicstart</span>) {</span>
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11476
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<pre style="margin: 0;">-<span id="LC11476" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">genomicstart - hit3->genomicstart</span>) + querylength5 + querylength3;</span>
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11491
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<pre style="margin: 0;">+<span id="LC11491" class="line" lang=""> } else if (hit3-><span class="idiff left right">high < hit5->low</span>) {</span>
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11492
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<pre style="margin: 0;">+<span id="LC11492" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">low - hit3->high</span>) + querylength5 + querylength3;</span>
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11477
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11493
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<pre style="margin: 0;"> <span id="LC11493" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
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11478
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11494
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<pre style="margin: 0;"> <span id="LC11494" class="line" lang=""> } else {</span>
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11479
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11495
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<pre style="margin: 0;"> <span id="LC11495" class="line" lang=""> new->insertlength = pair_insert_length_unpaired(hit5,hit3); /* was 0 */</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11504" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -11488,11 +11504,11 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11488
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11504
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<pre style="margin: 0;"> <span id="LC11504" class="line" lang=""> /* or 3-start..end and 5-end..start */</span>
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11489
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11505
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<pre style="margin: 0;"> <span id="LC11505" class="line" lang=""></span>
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11490
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11506
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<pre style="margin: 0;"> <span id="LC11506" class="line" lang=""> new->pair_relationship = 0;</span>
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11491
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<pre style="margin: 0;">-<span id="LC11491" class="line" lang=""> if (hit5-><span class="idiff left right">genomicstart < hit3->genomicstart</span>) {</span>
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11492
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<pre style="margin: 0;">-<span id="LC11492" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">genomicstart - hit5->genomicstart</span>) + querylength5 + querylength3;</span>
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11507
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<pre style="margin: 0;">+<span id="LC11507" class="line" lang=""> if (hit5-><span class="idiff left right">high < hit3->low</span>) {</span>
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11508
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<pre style="margin: 0;">+<span id="LC11508" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">low - hit5->high</span>) + querylength5 + querylength3;</span>
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11493
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11509
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<pre style="margin: 0;"> <span id="LC11509" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
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11494
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<pre style="margin: 0;">-<span id="LC11494" class="line" lang=""> } else if (hit3-><span class="idiff left right">genomicend < hit5->genomicend</span>) {</span>
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11495
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<pre style="margin: 0;">-<span id="LC11495" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">genomicend - hit3->genomicend</span>) + querylength5 + querylength3;</span>
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11510
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<pre style="margin: 0;">+<span id="LC11510" class="line" lang=""> } else if (hit3-><span class="idiff left right">high < hit5->low</span>) {</span>
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11511
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<pre style="margin: 0;">+<span id="LC11511" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">high - hit3->low</span>) + querylength5 + querylength3;</span>
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11496
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11512
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<pre style="margin: 0;"> <span id="LC11512" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
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11497
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11513
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<pre style="margin: 0;"> <span id="LC11513" class="line" lang=""> } else {</span>
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11498
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11514
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<pre style="margin: 0;"> <span id="LC11514" class="line" lang=""> new->insertlength = pair_insert_length_unpaired(hit5,hit3); /* was 0 */</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11625" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -11609,10 +11625,10 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11609
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11625
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<pre style="margin: 0;"> <span id="LC11625" class="line" lang=""> }</span>
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11610
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11626
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<pre style="margin: 0;"> <span id="LC11626" class="line" lang=""></span>
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11611
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11627
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<pre style="margin: 0;"> <span id="LC11627" class="line" lang=""> /* Have 5-start..end and 3-start..end */</span>
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11612
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<pre style="margin: 0;">-<span id="LC11612" class="line" lang=""> if (hit5-><span class="idiff left right">genomicend < hit3->genomicstart</span>) {</span>
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11628
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<pre style="margin: 0;">+<span id="LC11628" class="line" lang=""> if (hit5-><span class="idiff left right">high < hit3->low</span>) {</span>
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11613
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11629
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<pre style="margin: 0;"> <span id="LC11629" class="line" lang=""> /* No overlap */</span>
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11614
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11630
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<pre style="margin: 0;"> <span id="LC11630" class="line" lang=""> new->pair_relationship = +1;</span>
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11615
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<pre style="margin: 0;">-<span id="LC11615" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">genomicstart - hit5->genomicend</span>) + querylength5 + querylength3;</span>
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<td class="new_line diff-line-num new" data-linenumber="11631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11631
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<pre style="margin: 0;">+<span id="LC11631" class="line" lang=""> new->insertlength = (hit3-><span class="idiff left right">low - hit5->high</span>) + querylength5 + querylength3;</span>
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11616
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<td class="new_line diff-line-num" data-linenumber="11632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11632
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<pre style="margin: 0;"> <span id="LC11632" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
</pre>
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11617
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11633
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<pre style="margin: 0;"> <span id="LC11633" class="line" lang=""> debug10(printf("plus, no overlap: insert length %d = start3 %u - end5 %u + %d + %d\n",</span>
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11618
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11634
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<pre style="margin: 0;"> <span id="LC11634" class="line" lang=""> new->insertlength,hit3->genomicstart - hit3->chroffset,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11743" style="width: 35px; color: rgba(0,0,0,0.3); 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="11759" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -11743,10 +11759,10 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11743
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11759
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<pre style="margin: 0;"> <span id="LC11759" class="line" lang=""> }</span>
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11744
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11760
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<pre style="margin: 0;"> <span id="LC11760" class="line" lang=""></span>
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<td class="old_line diff-line-num" data-linenumber="11745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11745
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<td class="new_line diff-line-num" data-linenumber="11761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11761
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<pre style="margin: 0;"> <span id="LC11761" class="line" lang=""> /* Have 3-end..start and 5-end..start */</span>
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<td class="old_line diff-line-num old" data-linenumber="11746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11746
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<td class="new_line diff-line-num old" data-linenumber="11762" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC11746" class="line" lang=""> if (hit3-><span class="idiff left right">genomicstart < hit5->genomicend</span>) {</span>
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11762
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<pre style="margin: 0;">+<span id="LC11762" class="line" lang=""> if (hit3-><span class="idiff left right">high < hit5->low</span>) {</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11747
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<td class="new_line diff-line-num" data-linenumber="11763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11763
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<pre style="margin: 0;"> <span id="LC11763" class="line" lang=""> /* No overlap */</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11748
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11764
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<pre style="margin: 0;"> <span id="LC11764" class="line" lang=""> new->pair_relationship = -1;</span>
</pre>
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11749
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<pre style="margin: 0;">-<span id="LC11749" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">genomicend - hit3->genomicstart</span>) + querylength5 + querylength3;</span>
</pre>
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11765
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<pre style="margin: 0;">+<span id="LC11765" class="line" lang=""> new->insertlength = (hit5-><span class="idiff left right">low - hit3->high</span>) + querylength5 + querylength3;</span>
</pre>
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11750
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<td class="new_line diff-line-num" data-linenumber="11766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11766
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<pre style="margin: 0;"> <span id="LC11766" class="line" lang=""> new->insertlength_expected_sign = insertlength_expected(new->insertlength);</span>
</pre>
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11751
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11767
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<pre style="margin: 0;"> <span id="LC11767" class="line" lang=""> debug10(printf("minus, no overlap: insert length %d = end5 %u - start3 %u + %d + %d\n",</span>
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11752
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11768
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<pre style="margin: 0;"> <span id="LC11768" class="line" lang=""> new->insertlength,hit5->genomicend - hit5->chroffset,</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13456" style="width: 35px; color: rgba(0,0,0,0.3); 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="13472" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -13456,7 +13472,12 @@ Stage3pair_remove_overlaps (List_T hitpairlist, Hitlistpool_T hitlistpool,</td>
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13456
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13472
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<pre style="margin: 0;"> <span id="LC13472" class="line" lang=""> /* Prune based on nmatches adjusted by score to get a tradeoff between matches and parsimony */</span>
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13457
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13473
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<pre style="margin: 0;"> <span id="LC13473" class="line" lang=""> /* Same as step 1 of Stage3pair_optimal_score_final */</span>
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13458
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13474
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<pre style="margin: 0;"> <span id="LC13474" class="line" lang=""> debug8(printf(" Step 3. Maximize nmatches adjusted by score (with slop)\n"));</span>
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13459
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<td class="new_line diff-line-num old" data-linenumber="13475" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC13459" class="line" lang=""> optimal = (List_T) NULL;</span>
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13475
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<pre style="margin: 0;">+<span id="LC13475" class="line" lang=""> if (hitpairlist == NULL) {</span>
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13476
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<pre style="margin: 0;">+<span id="LC13476" class="line" lang=""> return (List_T) NULL;</span>
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13477
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<pre style="margin: 0;">+<span id="LC13477" class="line" lang=""> } else {</span>
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13478
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<pre style="margin: 0;">+<span id="LC13478" class="line" lang=""> optimal = (List_T) NULL;</span>
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13479
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<pre style="margin: 0;">+<span id="LC13479" class="line" lang=""> }</span>
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13480
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<pre style="margin: 0;">+<span id="LC13480" class="line" lang=""> </span>
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13460
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13481
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<pre style="margin: 0;"> <span id="LC13481" class="line" lang=""></span>
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13461
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13482
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<pre style="margin: 0;"> <span id="LC13482" class="line" lang=""> keptp = false;</span>
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13462
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13483
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<pre style="margin: 0;"> <span id="LC13483" class="line" lang=""> hitpairs = (Stage3pair_T *) List_to_array_n(&n,hitpairlist);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13535" style="width: 35px; color: rgba(0,0,0,0.3); 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="13556" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -13535,13 +13556,16 @@ Stage3pair_remove_overlaps (List_T hitpairlist, Hitlistpool_T hitlistpool,</td>
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13535
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13556
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<pre style="margin: 0;"> <span id="LC13556" class="line" lang=""> }</span>
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13536
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13557
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<pre style="margin: 0;"> <span id="LC13557" class="line" lang=""> FREE(hitpairs);</span>
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13537
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13558
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<pre style="margin: 0;"> <span id="LC13558" class="line" lang=""> FREE(eliminate);</span>
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13538
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<pre style="margin: 0;">-<span id="LC13538" class="line" lang=""> hitpairlist = optimal;</span>
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13539
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<pre style="margin: 0;">-<span id="LC13539" class="line" lang=""></span>
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13559
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<pre style="margin: 0;">+<span id="LC13559" class="line" lang=""> if ((hitpairlist = optimal) == NULL) {</span>
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13560
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<pre style="margin: 0;">+<span id="LC13560" class="line" lang=""> return (List_T) NULL;</span>
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13561
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<pre style="margin: 0;">+<span id="LC13561" class="line" lang=""> } else {</span>
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13562
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<pre style="margin: 0;">+<span id="LC13562" class="line" lang=""> optimal = (List_T) NULL;</span>
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13563
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<pre style="margin: 0;">+<span id="LC13563" class="line" lang=""> }</span>
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13564
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<pre style="margin: 0;">+<span id="LC13564" class="line" lang=""> </span>
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13540
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13565
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<pre style="margin: 0;"> <span id="LC13565" class="line" lang=""></span>
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13541
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13566
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<pre style="margin: 0;"> <span id="LC13566" class="line" lang=""> /* Eliminate within loci: minimize nsegments and maximize splice score (for approximately equal insertlengths) */</span>
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13542
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13567
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<pre style="margin: 0;"> <span id="LC13567" class="line" lang=""> /* Since we have achieved same number of matches, we should minimize nsegments to achieve parsimony */</span>
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13543
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13568
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<pre style="margin: 0;"> <span id="LC13568" class="line" lang=""> debug8(printf(" Step 4. Minimize nsegments and splice score (for approximately equal insertlengths)\n"));</span>
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13544
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<pre style="margin: 0;">-<span id="LC13544" class="line" lang=""> optimal = (List_T) NULL;</span>
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13545
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13569
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<pre style="margin: 0;"> <span id="LC13569" class="line" lang=""></span>
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13546
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13570
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<pre style="margin: 0;"> <span id="LC13570" class="line" lang=""> keptp = false;</span>
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13547
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13571
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<pre style="margin: 0;"> <span id="LC13571" class="line" lang=""> hitpairs = (Stage3pair_T *) List_to_array_n(&n,hitpairlist);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13644" style="width: 35px; color: rgba(0,0,0,0.3); 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="13668" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -13644,12 +13668,15 @@ Stage3pair_remove_overlaps (List_T hitpairlist, Hitlistpool_T hitlistpool,</td>
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13644
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13668
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<pre style="margin: 0;"> <span id="LC13668" class="line" lang=""> }</span>
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13645
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13669
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<pre style="margin: 0;"> <span id="LC13669" class="line" lang=""> FREE(hitpairs);</span>
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13646
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13670
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<pre style="margin: 0;"> <span id="LC13670" class="line" lang=""> FREE(eliminate);</span>
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13647
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<pre style="margin: 0;">-<span id="LC13647" class="line" lang=""> hitpairlist = optimal;</span>
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13648
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<pre style="margin: 0;">-<span id="LC13648" class="line" lang=""></span>
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13671
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<pre style="margin: 0;">+<span id="LC13671" class="line" lang=""> if ((hitpairlist = optimal) == NULL) {</span>
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13672
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<pre style="margin: 0;">+<span id="LC13672" class="line" lang=""> return (List_T) NULL;</span>
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13673
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<pre style="margin: 0;">+<span id="LC13673" class="line" lang=""> } else {</span>
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13674
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<pre style="margin: 0;">+<span id="LC13674" class="line" lang=""> optimal = (List_T) NULL;</span>
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13675
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<pre style="margin: 0;">+<span id="LC13675" class="line" lang=""> }</span>
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13676
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<pre style="margin: 0;">+<span id="LC13676" class="line" lang=""> </span>
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13649
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13677
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<pre style="margin: 0;"> <span id="LC13677" class="line" lang=""></span>
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13650
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13678
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<pre style="margin: 0;"> <span id="LC13678" class="line" lang=""> /* Eliminate within loci: minimize outerlength */</span>
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13651
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13679
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<pre style="margin: 0;"> <span id="LC13679" class="line" lang=""> debug8(printf(" Step 5. Minimize outerlength\n"));</span>
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13652
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<pre style="margin: 0;">-<span id="LC13652" class="line" lang=""> optimal = (List_T) NULL;</span>
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13653
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13680
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<pre style="margin: 0;"> <span id="LC13680" class="line" lang=""></span>
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13654
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13681
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<pre style="margin: 0;"> <span id="LC13681" class="line" lang=""> keptp = false;</span>
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13655
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13682
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<pre style="margin: 0;"> <span id="LC13682" class="line" lang=""> hitpairs = (Stage3pair_T *) List_to_array_n(&n,hitpairlist);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14558" style="width: 35px; color: rgba(0,0,0,0.3); 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="14585" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -14558,8 +14585,11 @@ Stage3pair_optimal_score_final_old (bool *eliminatedp, List_T hitpairlist,</td>
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14558
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14585
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<pre style="margin: 0;"> <span id="LC14585" class="line" lang=""> }</span>
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14559
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14586
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<pre style="margin: 0;"> <span id="LC14586" class="line" lang=""> }</span>
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14560
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14587
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<pre style="margin: 0;"> <span id="LC14587" class="line" lang=""> Hitlist_free(&hitpairlist);</span>
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14561
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<pre style="margin: 0;">-<span id="LC14561" class="line" lang=""> hitpairlist = optimal;</span>
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14562
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<pre style="margin: 0;">-<span id="LC14562" class="line" lang=""> optimal = (List_T) NULL;</span>
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14588
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<pre style="margin: 0;">+<span id="LC14588" class="line" lang=""> if ((hitpairlist = optimal) == NULL) {</span>
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14589
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<pre style="margin: 0;">+<span id="LC14589" class="line" lang=""> return (List_T) NULL;</span>
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14590
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<pre style="margin: 0;">+<span id="LC14590" class="line" lang=""> } else {</span>
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14591
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<pre style="margin: 0;">+<span id="LC14591" class="line" lang=""> optimal = (List_T) NULL;</span>
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14592
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<pre style="margin: 0;">+<span id="LC14592" class="line" lang=""> }</span>
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14563
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14593
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<pre style="margin: 0;"> <span id="LC14593" class="line" lang=""></span>
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14564
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14594
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<pre style="margin: 0;"> <span id="LC14594" class="line" lang=""></span>
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14565
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14595
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<pre style="margin: 0;"> <span id="LC14595" class="line" lang=""> /* Eliminate within loci (1): refalt_nmatches_to_trims_only */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14629" style="width: 35px; color: rgba(0,0,0,0.3); 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="14659" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -14629,8 +14659,11 @@ Stage3pair_optimal_score_final_old (bool *eliminatedp, List_T hitpairlist,</td>
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14629
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14659
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<pre style="margin: 0;"> <span id="LC14659" class="line" lang=""> }</span>
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14630
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14660
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<pre style="margin: 0;"> <span id="LC14660" class="line" lang=""> FREE(hitpairs);</span>
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14631
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14661
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<pre style="margin: 0;"> <span id="LC14661" class="line" lang=""> FREE(eliminate);</span>
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14632
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<pre style="margin: 0;">-<span id="LC14632" class="line" lang=""> hitpairlist = optimal;</span>
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14633
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<pre style="margin: 0;">-<span id="LC14633" class="line" lang=""> optimal = (List_T) NULL;</span>
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14662
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<pre style="margin: 0;">+<span id="LC14662" class="line" lang=""> if ((hitpairlist = optimal) == NULL) {</span>
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14663
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<pre style="margin: 0;">+<span id="LC14663" class="line" lang=""> return (List_T) NULL;</span>
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14664
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<pre style="margin: 0;">+<span id="LC14664" class="line" lang=""> } else {</span>
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14665
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<pre style="margin: 0;">+<span id="LC14665" class="line" lang=""> optimal = (List_T) NULL;</span>
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14666
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<pre style="margin: 0;">+<span id="LC14666" class="line" lang=""> }</span>
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14634
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14667
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<pre style="margin: 0;"> <span id="LC14667" class="line" lang=""></span>
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14635
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14668
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<pre style="margin: 0;"> <span id="LC14668" class="line" lang=""></span>
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14636
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14669
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<pre style="margin: 0;"> <span id="LC14669" class="line" lang=""> /* Eliminate within loci (2): nsegments and splice score */</span>
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<li id="aeb285890115a453e6448fd7de6fc67bf8daf3a4">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/ce9d89b0c6ca9fb5a12438e9894755cb3c4f24d6...34b6845fcfbcbb2cc7acd1fd140c92c15e52fcbc#aeb285890115a453e6448fd7de6fc67bf8daf3a4"><strong>src/substring.c</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: substring.c 223<span class="idiff left">553</span> 202<span class="idiff right">0-11-16 01:27:22</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: substring.c 223<span class="idiff left">818</span> 202<span class="idiff right">1-02-23 07:38:29</span>Z twu $"</span><span class="p">;</span></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="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></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="c"><span class="cp" style="color: #999; font-weight: 600;">#include "config.h"</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -1780,11 +1780,13 @@ Substring_new (int nmismatches, int ref_nmismatches, Univcoord_T left,</td>
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querystart_chrbound</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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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querystart_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">left</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1783" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* new->genomicstart += new->querystart_chrbound; */</span></span>
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1784
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<pre style="margin: 0;"> <span id="LC1784" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chrhigh</span><span class="p">)</span> <span class="p">{</span></span>
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1785
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1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">queryend_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1787
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1788
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<pre style="margin: 0;"> <span id="LC1788" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">queryend_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrhigh</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">left</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* new->genomicend -= (querylength - new->queryend_chrbound); */</span></span>
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="c"> <span class="p">}</span></span>
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1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="c"></span>
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1792
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<pre style="margin: 0;"> <span id="LC1792" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1795,11 +1797,13 @@ Substring_new (int nmismatches, int ref_nmismatches, Univcoord_T left,</td>
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1797
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<pre style="margin: 0;"> <span id="LC1797" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querystart_chrbound</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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1796
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1798
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<pre style="margin: 0;"> <span id="LC1798" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querystart_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chrhigh</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1800" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* new->genomicstart -= new->querystart_chrbound; */</span></span>
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1798
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1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="c"> <span class="p">}</span></span>
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1799
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1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span><span class="p">)</span> <span class="p">{</span></span>
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1800
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1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">queryend_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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1801
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1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1802
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1805
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<pre style="margin: 0;"> <span id="LC1805" class="line" lang="c"> <span class="n" style="color: #333;">new</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">queryend_chrbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">;</span></span>
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1806
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<pre style="margin: 0;">+<span id="LC1806" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* new->genomicend += (querylength - new->queryend_chrbound); */</span></span>
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1803
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1807
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<pre style="margin: 0;"> <span id="LC1807" class="line" lang="c"> <span class="p">}</span></span>
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1804
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1808
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<pre style="margin: 0;"> <span id="LC1808" class="line" lang="c"> <span class="p">}</span></span>
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1805
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1809
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<pre style="margin: 0;"> <span id="LC1809" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2334" style="width: 35px; color: rgba(0,0,0,0.3); 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="2338" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2334,11 +2338,13 @@ Substring_new_simple (int nmismatches, Univcoord_T left, int querystart, int que</td>
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2334
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2338
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<pre style="margin: 0;"> <span id="LC2338" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->querystart_chrbound = 0;</span></span>
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2335
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2339
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<pre style="margin: 0;"> <span id="LC2339" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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2336
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2340
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<pre style="margin: 0;"> <span id="LC2340" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->querystart_chrbound = chroffset - left;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2341
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<pre style="margin: 0;">+<span id="LC2341" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* new->genomicstart += new->querystart_chrbound; */</span></span>
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2337
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2342
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<pre style="margin: 0;"> <span id="LC2342" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2338
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2343
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<pre style="margin: 0;"> <span id="LC2343" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if (left + querylength < chrhigh) {</span></span>
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2339
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2344
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<pre style="margin: 0;"> <span id="LC2344" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->queryend_chrbound = querylength;</span></span>
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2340
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2345
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<pre style="margin: 0;"> <span id="LC2345" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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2341
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2346
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<pre style="margin: 0;"> <span id="LC2346" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->queryend_chrbound = chrhigh - left;</span></span>
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2347
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<pre style="margin: 0;">+<span id="LC2347" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* new->genomicend -= (querylength - new->queryend_chrbound); */</span></span>
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2342
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2348
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<pre style="margin: 0;"> <span id="LC2348" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2343
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2349
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<pre style="margin: 0;"> <span id="LC2349" class="line" lang="c"></span>
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2344
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2350
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<pre style="margin: 0;"> <span id="LC2350" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2349,11 +2355,13 @@ Substring_new_simple (int nmismatches, Univcoord_T left, int querystart, int que</td>
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2349
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2355
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<pre style="margin: 0;"> <span id="LC2355" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->querystart_chrbound = 0;</span></span>
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2350
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2356
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<pre style="margin: 0;"> <span id="LC2356" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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2351
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2357
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<pre style="margin: 0;"> <span id="LC2357" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->querystart_chrbound = (left + querylength) - chrhigh;</span></span>
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2358
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<pre style="margin: 0;">+<span id="LC2358" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* new->genomicstart -= new->querystart_chrbound; */</span></span>
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<td class="old_line diff-line-num" data-linenumber="2352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2352
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<td class="new_line diff-line-num" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2359
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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<td class="old_line diff-line-num" data-linenumber="2353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2353
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2360
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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> if (left + querylength > chroffset + querylength) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="2354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2354
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<td class="new_line diff-line-num" data-linenumber="2361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->queryend_chrbound = querylength;</span></span>
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2355
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2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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2356
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2363
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> new->queryend_chrbound = (left + querylength) - chroffset;</span></span>
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2364
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<pre style="margin: 0;">+<span id="LC2364" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* new->genomicend += (querylength - new->queryend_chrbound); */</span></span>
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2357
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2365
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<pre style="margin: 0;"> <span id="LC2365" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2358
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2366
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<pre style="margin: 0;"> <span id="LC2366" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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2359
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2367
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<pre style="margin: 0;"> <span id="LC2367" class="line" lang="c"></span>
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