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GitLab

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<div class="content">

<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/608e890aea0715b35fe55c634be918438223168e">608e890a</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:31:54+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.7.1+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/4c2ad7a854453bd66aee85bc22d16ba06323f9e3">4c2ad7a8</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:32:01+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.7.1+dfsg'

Update to upstream version '1.7.1+dfsg'

with Debian dir 2ab1c0abd9cb9dd4a0aed98f8f528d7620dcf3d1</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/9af8864ddeefd9ad8ed4722aa2e08d81cc2d5743">9af8864d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:32:01+02:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/5ca91b4a827629b8125b545428e58c4b15c0ce0a">5ca91b4a</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:32:01+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/558946ebda3d7832b7fd8c386f5c1622ca19fd19">558946eb</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:34:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/23f8e2244fd751b686b6e94b34d0f33ad3b705ad">23f8e224</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:34:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.5

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/canu/commit/b0bd43c00403591d5484a22a0d23e960204e8fad">b0bd43c0</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:39:47+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>22 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

debian/compat

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#0a6efeceaf747d1c3e0cc0c54e4fadd6ddc9de9a">

src/AS_UTL/stddev.H

</a>

</li>

<li class="file-stats">

<a href="#a54fef1f144954393f7213af443540839f62d26f">

src/bogart/AS_BAT_BestOverlapGraph.C

</a>

</li>

<li class="file-stats">

<a href="#ea5e534f631b45e7e7797aee707dcc10293b52fb">

src/bogart/AS_BAT_BestOverlapGraph.H

</a>

</li>

<li class="file-stats">

<a href="#f3c182a130e42ede38bcb662af9dd061ae944fa7">

src/bogart/AS_BAT_DropDeadEnds.C

</a>

</li>

<li class="file-stats">

<a href="#666fb6bea07a09d2c992eed6c59c01f22bd11fbd">

src/bogart/AS_BAT_MarkRepeatReads.C

</a>

</li>

<li class="file-stats">

<a href="#0fa925bec9836119b1b886b5b460cad7b819a443">

src/bogart/AS_BAT_MergeOrphans.C

</a>

</li>

<li class="file-stats">

<a href="#0acc7699c39da65041f5aa86bb4505bdccb840ab">

src/bogart/AS_BAT_OptimizePositions.C

</a>

</li>

<li class="file-stats">

<a href="#80d80b4dca5a701d2ccaf42d170bdc564315dfe7">

src/bogart/AS_BAT_OverlapCache.C

</a>

</li>

<li class="file-stats">

<a href="#bdb859bee1536bade4d2c27e546c1ed397b0d93d">

src/bogart/AS_BAT_PlaceContains.C

</a>

</li>

<li class="file-stats">

<a href="#afe103f609fd2a6e84ded26153c9411bd4265e9f">

src/bogart/AS_BAT_PopulateUnitig.C

</a>

</li>

<li class="file-stats">

<a href="#bd441caac58d9b73f15ae842113848828869ce32">

src/bogart/AS_BAT_Unitig.H

</a>

</li>

<li class="file-stats">

<a href="#785523ef798e0c6ec8990d8bf4a76216dbc5f373">

src/canu_version_update.pl

</a>

</li>

<li class="file-stats">

<a href="#37f197c29a6f3776ccaf400a51d8efdfbb79af21">

src/overlapErrorAdjustment/findErrors-Read_Frags.C

</a>

</li>

<li class="file-stats">

<a href="#b94ee93cab4ade098360f99895c9e7b4ff7bd114">

src/overlapErrorAdjustment/findErrors-Read_Olaps.C

</a>

</li>

<li class="file-stats">

<a href="#e16a09a812c43c51f5e5e85e9236de450fa6be09">

src/overlapErrorAdjustment/findErrors.C

</a>

</li>

<li class="file-stats">

<a href="#f6e23366bcce102996f2e38e40ac18feb1f78723">

src/overlapErrorAdjustment/findErrors.H

</a>

</li>

<li class="file-stats">

<a href="#5968ef8e04a03bc22f685551138c5e796da880c0">

src/pipelines/canu/Defaults.pm

</a>

</li>

<li class="file-stats">

<a href="#6a1192e790904d7df30212037b58266d09e0eace">

src/pipelines/canu/OverlapErrorAdjustment.pm

</a>

</li>

<li class="file-stats">

<a href="#23da18f1c1a1c22da72b64d5a004a6dd361e2681">

src/stores/ovStore.C

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

</td>

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">canu (1.7.1+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

</tr>

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

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

</td>

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

2

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

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

3

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

</td>

</tr>

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

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

</td>

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

4

</td>

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

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

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

</td>

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

5

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * debhelper 11</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  * Standards-Version: 4.1.5</span>

</pre>

</td>

</tr>

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

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

</td>

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

8

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

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

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 17 Jul 2018 12:34:50 +0200</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

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

</pre>

</td>

</tr>

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

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

1

</td>

<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">canu (1.7+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

</tr>

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

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

2

</td>

<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

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

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

</pre>

</td>

</tr>

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

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

3

</td>

<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

</td>

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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1

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

1

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

</pre>

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2

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

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5

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Afif Elghraoui <afif@debian.org></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">      debhelper (>= 10),</span>

</pre>

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8

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">      libboost-dev,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">      libmeryl-dev,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

5

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

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">               libboost-dev,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">               libmeryl-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># For File::Path</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">     libfilesys-df-perl,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">     mhap (>= 2.1.3)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.1.3</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">               libfilesys-df-perl,</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">               mhap (>= 2.1.3)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.1.5</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/canu</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/canu.git</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: http://canu.readthedocs.org/en/latest/</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/canu.git</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/canu.git</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: canu</span>

</pre>

</td>

</tr>

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

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

19

</td>

<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

</td>

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Depends:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">     ${shlibs:Depends},</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">     ${misc:Depends},</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">     ${perl:Depends},</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">     libfilesys-df-perl,</span>

</pre>

</td>

</tr>

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

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

25

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">     mhap (>= 2.1.3),</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">     gnuplot,</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Suggests:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">     pbgenomicconsensus,</span>

</pre>

</td>

</tr>

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

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

29

</td>

<td class="diff-line-num new_line old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">     nanopolish,</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">         ${perl:Depends},</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">         libfilesys-df-perl,</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">         mhap (>= 2.1.3),</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">         gnuplot</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Suggests: pbgenomicconsensus,</span>

</pre>

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26

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

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Description: single molecule sequence assembler for genomes</span>

</pre>

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31

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> Canu is a fork of the Celera Assembler, designed for high-noise</span>

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> single-molecule sequencing (such as the PacBio RS II or Oxford</span>

</pre>

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</table>

<br>

</li>

<li id="0a6efeceaf747d1c3e0cc0c54e4fadd6ddc9de9a">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#0a6efeceaf747d1c3e0cc0c54e4fadd6ddc9de9a"><strong>src/AS_UTL/stddev.H</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -286,7 +286,7 @@ computeExponentialMovingAverage(TT alpha, TT ema, TT value) {</td>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">template<typename TT></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">class genericStatistics {</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); 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="338" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -338,12 +338,12 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  vector<uint64>    &histogram(void) {    //  Returns pointer to private histogram data</span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    finalizeData();</span></span>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">_histogram</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(_histogram);</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  };</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  vector<uint64>    &Nstatistics(void) {  //  Returns pointer to private N data</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    finalizeData();</span></span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">_Nstatistics</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(_Nstatistics);</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  };</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  void               finalizeData(void) {</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">@@ -375,7 +375,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  vector<uint64>  _Nstatistics;</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">};</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC381" 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">@@ -422,12 +422,12 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  vector<uint64>    &histogram(void) {    //  Returns pointer to private histogram data</span></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    finalizeData();</span></span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(<span class="idiff left right">&</span>_histogram);</span></span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(_histogram);</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  };</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  vector<uint64>    &Nstatistics(void) {  //  Returns pointer to private N data</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    finalizeData();</span></span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(<span class="idiff left right">&</span>_Nstatistics);</span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return(_Nstatistics);</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  };</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="c"></span>

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</li>

<li id="a54fef1f144954393f7213af443540839f62d26f">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#a54fef1f144954393f7213af443540839f62d26f"><strong>src/bogart/AS_BAT_BestOverlapGraph.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -130,6 +130,27 @@ BestOverlapGraph::removeHighErrorBestEdges(void) {</td>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b5</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="n" style="color: #333;">edgeStats</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">erates</span><span class="p">[</span><span class="n" style="color: #333;">eratesLen</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b5</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">erate</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span>   <span class="n" style="color: #333;">edgeStats</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">erates</span><span class="p">[</span><span class="n" style="color: #333;">eratesLen</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">erate</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  If there are NO best edges, find the overlap with the most matches and use that.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

135

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">b5</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c">        <span class="p">(</span><span class="n" style="color: #333;">b3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>      <span class="n" style="color: #333;">no</span>    <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c">      <span class="n" style="color: #333;">BAToverlap</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ovl</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getOverlaps</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span> <span class="n" style="color: #333;">no</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>      <span class="n" style="color: #333;">bestM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c">      <span class="kt" style="color: #458; font-weight: 600;">double</span>      <span class="n" style="color: #333;">bestE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">oo</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">oo</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">no</span><span class="p">;</span> <span class="n" style="color: #333;">oo</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">double</span>  <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">erate</span><span class="p">())</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">RI</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">overlapLength</span><span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_iid</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestM</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">matches</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c">          <span class="n" style="color: #333;">bestM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c">          <span class="n" style="color: #333;">bestE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">erate</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">no</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c">        <span class="n" style="color: #333;">edgeStats</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">erates</span><span class="p">[</span><span class="n" style="color: #333;">eratesLen</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestE</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c">  <span class="n" style="color: #333;">_mean</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edgeStats</span><span class="p">.</span><span class="n" style="color: #333;">mean</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">@@ -357,6 +378,53 @@ BestOverlapGraph::removeSpurs(const char *prefix) {</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Mark zombie masters.  Any read that has only contained overlaps (it is the container) and is the</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  smallest ID of those with no hangs, is a master.  These get promoted to unitigs.</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="c"><span class="n" style="color: #333;">BestOverlapGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">findZombies</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">fiLimit</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RI</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numReads</span><span class="p">();</span></span>

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387

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">numThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">omp_get_max_threads</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">blockSize</span>  <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fiLimit</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numThreads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numThreads</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fiLimit</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">99</span><span class="p">;</span></span>

</pre>

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389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp parallel for schedule(dynamic, blockSize)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">fi</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;">fi</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">fiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

392

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>      <span class="n" style="color: #333;">no</span>  <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

393

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="c">    <span class="n" style="color: #333;">BAToverlap</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ovl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getOverlaps</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span> <span class="n" style="color: #333;">no</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

394

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>      <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">no</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

399

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">no</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>       <span class="c1" style="color: #998; font-style: italic;">//  If any overlap makes A not</span></span>

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<td class="diff-line-num new new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">AisContainer</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span>     <span class="c1" style="color: #998; font-style: italic;">//  a container, it's not a zombie</span></span>

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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="c">        <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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402

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="c"></span>

</pre>

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403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">no</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="c">    <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">no</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span>             <span class="c1" style="color: #998; font-style: italic;">//  Find the smallest ID</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span>             <span class="c1" style="color: #998; font-style: italic;">//  with no hangs.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="c">          <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="c">          <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nc</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="c">        <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

413

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nc</span><span class="p">)</span> <span class="p">{</span>                             <span class="c1" style="color: #998; font-style: italic;">//  If we're smaller, we're a</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp critical (suspInsert)              //  Zombie Master!</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

416

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="c">      <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"read %u is a zombie.</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;">fi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="c">        <span class="n" style="color: #333;">_zombie</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

422

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c">  <span class="n" style="color: #333;">writeStatus</span><span class="p">(</span><span class="s" style="color: #d14;">"BestOverlapGraph()-- detected "</span> <span class="n" style="color: #333;">F_SIZE_T</span> <span class="s" style="color: #d14;">" zombie reads.</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;">_zombie</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

424

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

<pre style="margin: 0;">+<span id="LC424" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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

<pre style="margin: 0;">+<span id="LC425" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

426

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

<pre style="margin: 0;">+<span id="LC426" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

427

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

<pre style="margin: 0;">+<span id="LC427" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

360

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<td class="diff-line-num new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

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

<pre style="margin: 0;"> <span id="LC428" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

361

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<td class="diff-line-num new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

429

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

<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"><span class="n" style="color: #333;">BestOverlapGraph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">findEdges</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

362

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<td class="diff-line-num new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

430

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">fiLimit</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RI</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numReads</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -513,6 +581,8 @@ BestOverlapGraph::BestOverlapGraph(double        erateGraph,</td>

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<td class="diff-line-num old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

513

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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c">    <span class="n" style="color: #333;">findEdges</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

514

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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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

<pre style="margin: 0;"> <span id="LC582" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

515

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<td class="diff-line-num new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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

<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c">  <span class="n" style="color: #333;">findZombies</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

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

<pre style="margin: 0;">+<span id="LC585" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

516

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<td class="diff-line-num new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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

<pre style="margin: 0;"> <span id="LC586" class="line" lang="c">  <span class="n" style="color: #333;">reportBestEdges</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">logFileFlagSet</span><span class="p">(</span><span class="n" style="color: #333;">LOG_ALL_BEST_EDGES</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"best.3.final"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"best"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

517

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<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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

<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

518

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<td class="diff-line-num new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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<pre style="margin: 0;"> <span id="LC588" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  One more pass, to find any ambiguous best edges.</span></span>

</pre>

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<br>

</li>

<li id="ea5e534f631b45e7e7797aee707dcc10293b52fb">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#ea5e534f631b45e7e7797aee707dcc10293b52fb"><strong>src/bogart/AS_BAT_BestOverlapGraph.H</strong></a>

<hr>

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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">@@ -183,6 +183,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">removeSuspicious</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">removeSpurs</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">removeLopsidedEdges</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">findZombies</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">findEdges</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">_suspicious</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">readid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c">  <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c">  <span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isZombie</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">readid</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">_zombie</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">readid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c">  <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">reportEdgeStatistics</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">reportBestEdges</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">label</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -283,6 +288,7 @@ private:</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c">  <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span>                <span class="n" style="color: #333;">_suspicious</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c">  <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span>                <span class="n" style="color: #333;">_singleton</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c">  <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span>                <span class="n" style="color: #333;">_spur</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="c">  <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span>                <span class="n" style="color: #333;">_zombie</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c">  <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">BestOverlaps</span><span class="o" style="font-weight: 600;">></span>  <span class="n" style="color: #333;">_bestM</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c">  <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">BestScores</span><span class="o" style="font-weight: 600;">></span>    <span class="n" style="color: #333;">_scorM</span><span class="p">;</span></span>

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<br>

</li>

<li id="f3c182a130e42ede38bcb662af9dd061ae944fa7">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#f3c182a130e42ede38bcb662af9dd061ae944fa7"><strong>src/bogart/AS_BAT_DropDeadEnds.C</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">@@ -133,17 +133,16 @@ findPrevRead(Unitig *tig,</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"><span class="n" style="color: #333;">uint32</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">dropDeadFirstRead</span><span class="p">(</span><span class="n" style="color: #333;">AssemblyGraph</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">AG</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c">                  <span class="n" style="color: #333;">Unitig</span>        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">                  <span class="n" style="color: #333;">Unitig</span>        <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c">                  <span class="n" style="color: #333;">bool</span>           <span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c">  <span class="n" style="color: #333;">ufNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">firstRead</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">  <span class="n" style="color: #333;">ufNode</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findNextRead</span><span class="p">(</span><span class="n" style="color: #333;">tig</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c">   <span class="c1" style="color: #998; font-style: italic;">//  No next read, keep fn in the tig.</span></span>

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC143" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sn</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC144" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()- read %8u no sn</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;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sn</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Over all edges from the first read, look for any edge to something else.</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); 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="152" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -153,24 +152,36 @@ dropDeadFirstRead(AssemblyGraph *AG,</td>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  the tig.  We assume that this is always the first read, which is OK, because the function name</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  says so.  Any edge to anywhere means the read is good and should be kept.</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 1st read %8u has no edges</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c">    <span class="n" style="color: #333;">BestPlacement</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">)[</span><span class="n" style="color: #333;">pp</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC159" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- 1st read %8u %s pf %3u/%3u best5 %8u best3 %8u bestC %8u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC160" class="line" lang="c">             <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC161" class="line" lang="c">             <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"->"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<-"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC162" class="line" lang="c">             <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC163" class="line" lang="c">             <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">,</span> <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">,</span> <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">bestC</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">bestC</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 1st read %8u %s edge %4u/%-4u - contained in %u - confirmed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c">               <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c">               <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">               <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"->"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<-"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c">               <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c">               <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">bestC</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">);</span></span>

</pre>

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166

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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC170" class="line" lang="c">        <span class="p">((</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c">        <span class="p">((</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 1st read %8u %s edge %4u/%-4u - 5:%u 3:%u - confirmed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="c">               <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c">               <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c">               <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"->"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<-"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c">               <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c">               <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">,</span> <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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

</pre>

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184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  But no edge means we need to check the second read.  If it has an edge, then we infer the</span></span>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  first read is bogus and should be removed.  If it also has no edge (except to the first read,</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  duh) then we know nothing: this could be novel sequence or it could be the same garbage that</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -180,26 +191,41 @@ dropDeadFirstRead(AssemblyGraph *AG,</td>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  first read.  Well, and that if the second read has an edge we declare the first read to be</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  junk.  That's also a bit of a difference from the previous loop.</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 2nd read %8u has no edges - keep first</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span> <span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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

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

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

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">pp</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c">    <span class="n" style="color: #333;">BestPlacement</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">)[</span><span class="n" style="color: #333;">pp</span><span class="p">];</span></span>

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201

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

<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"></span>

</pre>

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

<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

186

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC186" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left">writeLog</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"dropDead()-- 2nd read %8u %s pf %3u/%3u best5 %8u best3 %8u bestC %8u</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

187

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC187" class="line" lang="c">      <span class="idiff left">       </span><span class="n" style="color: #333;"><span class="idiff">sn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">ident</span></span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

188

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC188" class="line" lang="c">             <span class="n" style="color: #333;"><span class="idiff left">sn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isForward</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"->"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"<-</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

189

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC189" class="line" lang="c">             <span class="n" style="color: #333;"><span class="idiff left">pp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AG</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getForward</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ident</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

190

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC190" class="line" lang="c">             <span class="n" style="color: #333;"><span class="idiff left">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">best5</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">best3</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

191

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<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC191" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

192

</td>

<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC192" class="line" lang="c">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ident</span></span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

202

</td>

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

<pre style="margin: 0;">+<span id="LC202" class="line" lang="c">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ident</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

203

</td>

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

<pre style="margin: 0;">+<span id="LC203" class="line" lang="c">      <span class="n" style="color: #333;"><span class="idiff left">writeLog</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"dropDead()-- (%s) 2nd read %8u %s edge %4u/%-4u - contained in %u - drop first</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

204

</td>

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

<pre style="margin: 0;">+<span id="LC204" class="line" lang="c">             <span class="idiff left">  </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">isForward</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"fwd"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"rev</span>"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

205

</td>

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

<pre style="margin: 0;">+<span id="LC205" class="line" lang="c">             <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">sn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">ident</span></span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

206

</td>

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

<pre style="margin: 0;">+<span id="LC206" class="line" lang="c">             <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">sn</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isForward</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"->"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"<-"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c">               <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c">    <span class="idiff left">           </span><span class="n" style="color: #333;"><span class="idiff">pf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bestC</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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194

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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC196" class="line" lang="c">        <span class="p">((</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c">        <span class="p">((</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 2nd read %8u %s edge %4u/%-4u - 5:%u 3:8u - drop first</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c">               <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c">               <span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="c">               <span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"->"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"<-"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="c">               <span class="n" style="color: #333;">pp</span><span class="p">,</span> <span class="n" style="color: #333;">AG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getForward</span><span class="p">(</span><span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c">               <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best5</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">,</span> <span class="n" style="color: #333;">pf</span><span class="p">.</span><span class="n" style="color: #333;">best3</span><span class="p">.</span><span class="n" style="color: #333;">b_iid</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Otherwise, the second read had only edges to the first read, and we should keep the first</span></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  read.</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="c">  <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- (%s) 2nd read %8u has no useful external edges - keep first</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">isForward</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"fwd"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"rev"</span><span class="p">,</span> <span class="n" style="color: #333;">sn</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -222,20 +248,32 @@ dropDeadEnds(AssemblyGraph  *AG,</td>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c">        <span class="p">(</span><span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_isUnassembled</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dropDeadFirstRead</span><span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="p">,</span> <span class="n" style="color: #333;">tig</span><span class="p">);</span>        <span class="c1" style="color: #998; font-style: italic;">//  Decide if the first read is junk.</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- testing tig %u length %u</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;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getLength</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

253

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

254

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dropDeadFirstRead</span><span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="p">,</span> <span class="n" style="color: #333;">tig</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">//  Decide if the first read is junk.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

255

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

256

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "drop dead for tig %u (flipped)\n", ti);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

257

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

227

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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

258

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c">    <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span>                       <span class="c1" style="color: #998; font-style: italic;">//  Flip.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

228

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<td class="diff-line-num new_line old" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dropDeadFirstRead</span><span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="p">,</span> <span class="n" style="color: #333;">tig</span><span class="p"><span class="idiff left">);</span></span><span class="idiff right">       </span> <span class="c1" style="color: #998; font-style: italic;">//  Decide if the last (now first) read is junk.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

259

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dropDeadFirstRead</span><span class="p">(</span><span class="n" style="color: #333;">AG</span><span class="p">,</span> <span class="n" style="color: #333;">tig</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff right">);</span></span> <span class="c1" style="color: #998; font-style: italic;">//  Decide if the last (now first) read is junk.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c">    <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">reverseComplement</span><span class="p">();</span>                       <span class="c1" style="color: #998; font-style: italic;">//  Flip back.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

261

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"></span>

</pre>

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

<td class="diff-line-num old old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

231

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<td class="diff-line-num new_line old" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC231" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span>                     <span class="c1" style="color: #998; font-style: italic;">//  Nothing to remove, just get out of here.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ln</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span>                   <span class="c1" style="color: #998; font-style: italic;">//  Nothing to remove, nothing to do.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

263

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- both ends confirmed</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

232

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<td class="diff-line-num new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

265

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

266

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

<pre style="margin: 0;">+<span id="LC266" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span> <span class="p">{</span>                                 <span class="c1" style="color: #998; font-style: italic;">//  The same thing to remove, ignore it.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- retaining spanning read %u</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;">fn</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

269

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

271

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

<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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<td class="diff-line-num new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  At least one read needs to be kicked out.  Make new tigs for everything.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

273

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff">   </span><span class="n" style="color: #333;"><span class="idiff">fnMsg</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">};</span></span><span class="idiff right">   </span><span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

237

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<td class="diff-line-num new_line old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff">   </span><span class="n" style="color: #333;"><span class="idiff">nnMsg</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">};</span></span><span class="idiff right">   </span><span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span>  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">nnOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff">   </span><span class="n" style="color: #333;"><span class="idiff">lnMsg</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">80</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">};</span></span><span class="idiff right">   </span><span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span>  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">nnOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">lnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

239

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

277

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

<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

240

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<td class="diff-line-num new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC278" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c">      <span class="n" style="color: #333;">fnTig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">newUnitig</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -256,32 +294,26 @@ dropDeadEnds(AssemblyGraph  *AG,</td>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Move reads to their new unitig.</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="c">    <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fnMsg</span><span class="p">,</span> <span class="s" style="color: #d14;">"                                      "</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c">    <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">nnMsg</span><span class="p">,</span> <span class="s" style="color: #d14;">"                          "</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="c">    <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">lnMsg</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tt</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">tt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">tt</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c">      <span class="n" style="color: #333;">ufNode</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span>        <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">ident</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fn</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">sprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fnMsg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"first read %9u to tig %7u --"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ident</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fnTig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">id</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">writeLog</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"dropDead()-- tig %u gets first read %u</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fnTig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">id</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ident</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c">        <span class="n" style="color: #333;">fnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addRead</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC304" 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;">read</span><span class="p">.</span><span class="n" style="color: #333;">ident</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ln</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">sprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lnMsg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-- last read %9u to tig %7u"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ident</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lnTig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">id</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">writeLog</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"dropDead()-- tig %u gets last read %u</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lnTig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">id</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ident</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c">        <span class="n" style="color: #333;">lnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addRead</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nnOff</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC276" class="line" lang="c">          <span class="n" style="color: #333;"><span class="idiff left">sprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nnMsg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"other reads to tig %7u</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">nnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c">          <span class="n" style="color: #333;"><span class="idiff left">writeLog</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"dropDead()-- tig %u gets all other reads</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">nnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c">          <span class="n" style="color: #333;">nnOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c">        <span class="n" style="color: #333;">nnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addRead</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nnOff</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDeadEnds()-- tig %7u --> %s %s %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;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">fnMsg</span><span class="p">,</span> <span class="n" style="color: #333;">nnMsg</span><span class="p">,</span> <span class="n" style="color: #333;">lnMsg</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fnTig</span><span class="p">)</span>  <span class="n" style="color: #333;">fnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cleanUp</span><span class="p">();</span>   <span class="c1" style="color: #998; font-style: italic;">//  Probably not neeeded, but cheap.</span></span>

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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lnTig</span><span class="p">)</span>  <span class="n" style="color: #333;">lnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cleanUp</span><span class="p">();</span>   <span class="c1" style="color: #998; font-style: italic;">//  Probably not neeeded, but cheap.</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nnTig</span><span class="p">)</span>  <span class="n" style="color: #333;">nnTig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cleanUp</span><span class="p">();</span>   <span class="c1" style="color: #998; font-style: italic;">//  Most likely needed.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); 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="324" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -292,6 +324,6 @@ dropDeadEnds(AssemblyGraph  *AG,</td>

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<td class="diff-line-num old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c">    <span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="c">  <span class="n" style="color: #333;">writeStatus</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead<span class="idiff left right">Ends</span>()-- Modified %u tigs.  Dropped %u first and %u last reads, %u tig%s had both reads dropped.</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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<pre style="margin: 0;">+<span id="LC327" class="line" lang="c">  <span class="n" style="color: #333;">writeStatus</span><span class="p">(</span><span class="s" style="color: #d14;">"dropDead()-- Modified %u tigs.  Dropped %u first and %u last reads, %u tig%s had both reads dropped.</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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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c">              <span class="n" style="color: #333;">numT</span><span class="p">,</span> <span class="n" style="color: #333;">numF</span><span class="p">,</span> <span class="n" style="color: #333;">numL</span><span class="p">,</span> <span class="n" style="color: #333;">numB</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">numB</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"s"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"><span class="p">}</span></span></pre>

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<br>

</li>

<li id="666fb6bea07a09d2c992eed6c59c01f22bd11fbd">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#666fb6bea07a09d2c992eed6c59c01f22bd11fbd"><strong>src/bogart/AS_BAT_MarkRepeatReads.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -702,12 +702,15 @@ findConfusedEdges(TigVector            &tigs,</td>

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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c">        <span class="n" style="color: #333;">uint32</span>   <span class="n" style="color: #333;">tgBid</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">rdBid</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="c">        <span class="c1" style="color: #998; font-style: italic;">//  If the read is in a singleton, skip.  These are unassembled crud.</span></span>

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<td class="diff-line-num new_line old" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC705" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">tgBid</span>                      <span class="idiff left right">   </span><span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">tgBid</span>                      <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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706

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<td class="diff-line-num new_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c">            <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">tgBid</span><span class="p">]</span>                <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<td class="diff-line-num new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="c">            <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">tgBid</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<td class="diff-line-num new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="c">          <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="diff-line-num new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<td class="diff-line-num new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="c">        <span class="c1" style="color: #998; font-style: italic;">//  Skip if this overlap is the best we're trying to match.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="c">        <span class="c1" style="color: #998; font-style: italic;">//</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="c">        <span class="c1" style="color: #998; font-style: italic;">//  NOTE.  This doesn't care about potential duplicate overlaps between a pair of reads,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c">        <span class="c1" style="color: #998; font-style: italic;">//  as we're looking for thicker overlaps off only one end of the read.</span></span>

</pre>

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711

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<td class="diff-line-num new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="c">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rdBid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b5</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">())</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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712

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<td class="diff-line-num new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="c">            <span class="p">(</span><span class="n" style="color: #333;">rdBid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readId</span><span class="p">()))</span></span>

</pre>

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713

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<td class="diff-line-num new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c">          <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="0fa925bec9836119b1b886b5b460cad7b819a443">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#0fa925bec9836119b1b886b5b460cad7b819a443"><strong>src/bogart/AS_BAT_MergeOrphans.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,8 +73,15 @@ typedef  map<uint32, vector<uint32> >  BubTargetList;</td>

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73

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73

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

76

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<td class="diff-line-num new_line old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Decide which tigs can be orphans.  Any unitig where (nearly) every dovetail read has an overlap</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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<td class="diff-line-num new_line old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  to some other unitig is a candidate for orphan popping.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Decide which tigs can be orphans.  Any unitig where (nearly) every dovetail</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  read has an overlap to some other unitig is a candidate for orphan popping.</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Counts the number of reads that have an overlap to some other tig</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  (tigOlapsTo).  if more than half the reads in the tig have an overlap to</span></span>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  some other tig, it is a potential place to pop the bubble.</span></span>

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82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Returns BubTargetList, a map of uint32 to vector<uint32>, of the potential</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  places that some tig could be popped into.</span></span>

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">findPotentialOrphans</span><span class="p">(</span><span class="n" style="color: #333;">TigVector</span>       <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tigs</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); 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="624" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -617,13 +624,16 @@ mergeOrphans(TigVector &tigs,</td>

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">candidatePop</span> <span class="o" style="font-weight: 600;">*></span>    <span class="n" style="color: #333;">targets</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC626" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">intervalList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">targetIntervals</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">targetIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="c">      <span class="n" style="color: #333;">saveCorrectlySizedInitialIntervals</span><span class="p">(</span><span class="n" style="color: #333;">orphan</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC621" class="line" lang="c">                                         <span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">],</span>     <span class="c1" style="color: #998; font-style: italic;">//  The targetID      in targetIntervals</span></span>

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<pre style="margin: 0;">-<span id="LC622" class="line" lang="c">                                         <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span>          <span class="c1" style="color: #998; font-style: italic;">//  The interval list in targetIntervals</span></span>

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<pre style="margin: 0;">-<span id="LC623" class="line" lang="c">                                         <span class="n" style="color: #333;">fReadID</span><span class="p">,</span></span>

</pre>

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624

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<td class="diff-line-num new_line old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC624" class="line" lang="c">                                         <span class="n" style="color: #333;">lReadID</span><span class="p">,</span></span>

</pre>

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625

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<td class="diff-line-num new_line old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC625" class="line" lang="c">                                         <span class="n" style="color: #333;">placed</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

626

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<td class="diff-line-num new_line old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC626" class="line" lang="c">                                         <span class="n" style="color: #333;">targets</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"mergeOrphans()-- orphan %u wants to go into nonexistent tig %u!</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;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="c">      <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c">        <span class="n" style="color: #333;">saveCorrectlySizedInitialIntervals</span><span class="p">(</span><span class="n" style="color: #333;">orphan</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

631

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="c">                                           <span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">],</span>     <span class="c1" style="color: #998; font-style: italic;">//  The targetID      in targetIntervals</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c">                                           <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">,</span>          <span class="c1" style="color: #998; font-style: italic;">//  The interval list in targetIntervals</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="c">                                           <span class="n" style="color: #333;">fReadID</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="c">                                           <span class="n" style="color: #333;">lReadID</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c">                                           <span class="n" style="color: #333;">placed</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c">                                           <span class="n" style="color: #333;">targets</span><span class="p">);</span></span>

</pre>

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637

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

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<td class="diff-line-num new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c">    <span class="n" style="color: #333;">targetIntervals</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span>   <span class="c1" style="color: #998; font-style: italic;">//  intervalList already freed.</span></span>

</pre>

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629

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639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); 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="667" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -657,7 +667,7 @@ mergeOrphans(TigVector &tigs,</td>

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657

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667

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="c">                   <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">placed</span><span class="p">[</span><span class="n" style="color: #333;">op</span><span class="p">].</span><span class="n" style="color: #333;">frgID</span><span class="p">,</span></span>

</pre>

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658

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<td class="diff-line-num new_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

668

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="c">                   <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">placed</span><span class="p">[</span><span class="n" style="color: #333;">op</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">placed</span><span class="p">[</span><span class="n" style="color: #333;">op</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>

</pre>

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659

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669

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

<pre style="margin: 0;"> <span id="LC669" class="line" lang="c"></span>

</pre>

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660

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<td class="diff-line-num new_line old" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC660" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"mergeOrphans()-- tig %8u length %9u -> target %8u piece %2u position %9u-%-9u length %8u - expected %3"</span> <span class="n" style="color: #333;">F_<span class="idiff left">SIZE_TP</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" reads, had %3"</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">F_SIZE_TP</span></span> <span class="s" style="color: #d14;">" reads.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"mergeOrphans()-- tig %8u length %9u -> target %8u piece %2u position %9u-%-9u length %8u - expected %3"</span> <span class="n" style="color: #333;">F_<span class="idiff left">U32</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" reads, had %3"</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">F_U32</span></span> <span class="s" style="color: #d14;">" reads.</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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671

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="c">               <span class="n" style="color: #333;">orphan</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">orphan</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getLength</span><span class="p">(),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="c">               <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">tt</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">targets</span><span class="p">[</span><span class="n" style="color: #333;">tt</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgn</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="c">               <span class="n" style="color: #333;">orphanSize</span><span class="p">,</span> <span class="n" style="color: #333;">targetSize</span><span class="p">);</span></span>

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<br>

</li>

<li id="0acc7699c39da65041f5aa86bb4505bdccb840ab">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#0acc7699c39da65041f5aa86bb4505bdccb840ab"><strong>src/bogart/AS_BAT_OptimizePositions.C</strong></a>

<hr>

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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">@@ -59,6 +59,77 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Decide if two reads in a tig are compatible with an overlap.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Returns true if the reads are overlapping in the tig, and are oriented consistent with the overlap.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="n" style="color: #333;">bool</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="n" style="color: #333;">Unitig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize_isCompatible</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span>       <span class="n" style="color: #333;">ii</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c">                              <span class="n" style="color: #333;">uint32</span>       <span class="n" style="color: #333;">jj</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c">                              <span class="n" style="color: #333;">BAToverlap</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">olap</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c">                              <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">inInit</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c">                              <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">secondPass</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c">                              <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c">  <span class="n" style="color: #333;">SeqInterval</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c">  <span class="n" style="color: #333;">SeqInterval</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">jp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c">  <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOvl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Decide if the overlap preserves the ordering in the tig.</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  This is of questionable value, and might be incorrect.  We can have two overlaps between</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  a pair of reads iff the orientation differs - the flipped flag.  That gets tested elsewhere.</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c">  <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOrdered</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c">  <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOvlLo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()));</span></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c">  <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOvlHi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()));</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//bool  isOvlLo = jp.min() < ip.min();   //  Is the above too rigorous?</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//bool  isOvlHi = ip.min() < jp.min();</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  isOvl tells the end of the read that should have the overlap (according to the tig layout),</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  so check if the overlap actually is on that end.  If not, flag this as 'mis ordered'.</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">isOvlLo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AEndIs5prime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c">      <span class="p">((</span><span class="n" style="color: #333;">isOvlLo</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isReverse</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AEndIs3prime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c">      <span class="p">((</span><span class="n" style="color: #333;">isOvlHi</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AEndIs3prime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c">      <span class="p">((</span><span class="n" style="color: #333;">isOvlHi</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isReverse</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AEndIs5prime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c">    <span class="n" style="color: #333;">isOrdered</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  But if in a containment relationship, it cannot be mis ordered.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AisContained</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AisContainer</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c">    <span class="n" style="color: #333;">isOrdered</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c">  <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOriented</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">flipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c">      <span class="p">((</span><span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">isForward</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">flipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c">    <span class="n" style="color: #333;">isOriented</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">secondPass</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize_%s()-- tig %7u read %9u (at %9d %9d) olap to read %9u (at %9d %9d) - hangs %7d %7d - %s %s ovlLo %d ovlHi %d contained %d container %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c">             <span class="p">(</span><span class="n" style="color: #333;">inInit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"initPlace"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"recompute"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c">             <span class="n" style="color: #333;">id</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c">             <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">,</span> <span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">ip</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c">             <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">,</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">jp</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c">             <span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">a_hang</span><span class="p">,</span> <span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">b_hang</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c">             <span class="p">(</span><span class="n" style="color: #333;">isOvl</span>     <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"overlapping"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"not-overlapping"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c">             <span class="p">(</span><span class="n" style="color: #333;">isOrdered</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"ordered"</span>     <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"mis-ordered"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c">             <span class="n" style="color: #333;">isOvlLo</span><span class="p">,</span> <span class="n" style="color: #333;">isOvlHi</span><span class="p">,</span> <span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AisContained</span><span class="p">(),</span> <span class="n" style="color: #333;">olap</span><span class="p">.</span><span class="n" style="color: #333;">AisContainer</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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

<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span><span class="p">((</span><span class="n" style="color: #333;">isOvl</span>      <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c">         <span class="p">(</span><span class="n" style="color: #333;">isOrdered</span>  <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c">         <span class="p">(</span><span class="n" style="color: #333;">isOriented</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

130

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

<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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

<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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

<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

</td>

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

63

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"><span class="n" style="color: #333;">Unitig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize_initPlace</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">ii</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c">                           <span class="n" style="color: #333;">optPos</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">op</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">@@ -87,37 +158,18 @@ Unitig::optimize_initPlace(uint32        ii,</td>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">uu</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span> <span class="p">(</span><span class="n" style="color: #333;">jid</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">jj</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpathIdx</span><span class="p">(</span><span class="n" style="color: #333;">jid</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Probably overkill, but report ALL overlaps for the troubling reads.</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">firstPass</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize_initPlace()-- olap %u a %u b %u hangs %d %d</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;">oo</span><span class="p">,</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">jid</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uu</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">id</span><span class="p">())</span>   <span class="c1" style="color: #998; font-style: italic;">//  Skip if the overlap is to a different tig.</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>       <span class="c1" style="color: #998; font-style: italic;">//  (the ufpathIdx() call is valid, but using it isn't)</span></span>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Reads are in the same tig.  Decide if they overlap in position.</span></span>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c">      <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">isOvl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Log!  beVerbose should be true for the second pass, but just in case it isn't.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

103

</td>

<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC103" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

104

</td>

<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC104" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">firstPass</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

</td>

<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC105" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize_initPlace()-- olap %4u tig %7u read %8u (at %9d %9d) olap to read %8u (at %9d %9d) - hangs %7d %7d - %s %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC106" class="line" lang="c">                 <span class="n" style="color: #333;">oo</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC107" class="line" lang="c">                 <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

108

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c">                 <span class="n" style="color: #333;">jid</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

109

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="c">                 <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC110" class="line" lang="c">                 <span class="p">(</span><span class="n" style="color: #333;">isOvl</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"overlapping"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"not-overlapping"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="c">                 <span class="p">(</span><span class="n" style="color: #333;">jj</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ii</span><span class="p">)</span>       <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"after"</span>       <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"before"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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

<pre style="margin: 0;">+<span id="LC161" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uu</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">id</span><span class="p">())</span>   <span class="c1" style="color: #998; font-style: italic;">//  Skip if to a different tig.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>       <span class="c1" style="color: #998; font-style: italic;">//  (otherwise, ufpath[jj] is invalid below)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

</td>

<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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

<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

</td>

<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isOvl</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span>            <span class="c1" style="color: #998; font-style: italic;">//  Skip if the reads</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

</td>

<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC114" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>                    <span class="c1" style="color: #998; font-style: italic;">//  don't overlap</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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

<pre style="margin: 0;">+<span id="LC164" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Skip if:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//    this is the first pass, but the overlap is to a read after us.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//    the overlap isn't compatible with the layout.</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC116" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">firstPass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">jj</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ii</span><span class="p">))</span>  <span class="c1" style="color: #998; font-style: italic;">//  We're setting initial positions, so overlaps to reads after</span></span>

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<td class="diff-line-num new_line old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC117" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>                    <span class="c1" style="color: #998; font-style: italic;">//  us aren't correct, unless we're in the 2nd pass</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">firstPass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">jj</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c">          <span class="p">(</span><span class="n" style="color: #333;">optimize_isCompatible</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">firstPass</span><span class="p">,</span> <span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Reads overlap.  Compute the position of the read using</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  the overlap and the other read.</span></span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Compute the position of the read using the overlap and the other read.</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">      <span class="n" style="color: #333;">nmin</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">fwd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c">      <span class="n" style="color: #333;">cnt</span>  <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,8 +228,9 @@ Unitig::optimize_recompute(uint32        iid,</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>       <span class="n" style="color: #333;">cnt</span>  <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %8u previous  - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span><span class="p">,</span>           <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %8u length    - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">readLen</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()--</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="diff-line-num new new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %9u previous  - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span><span class="p">,</span>           <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %9u length    - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">readLen</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Process all overlaps.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -187,26 +240,34 @@ Unitig::optimize_recompute(uint32        iid,</td>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">uu</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span> <span class="p">(</span><span class="n" style="color: #333;">jid</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">jj</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpathIdx</span><span class="p">(</span><span class="n" style="color: #333;">jid</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC190" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uu</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">id</span><span class="p">())</span>   <span class="c1" style="color: #998; font-style: italic;">//  Skip if the overlap is to a different tig.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>       <span class="c1" style="color: #998; font-style: italic;">//  (the ufpathIdx() call is valid, but using it isn't)</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

193

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<td class="diff-line-num new_line old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC193" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;">//  Skip if the reads</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="diff-line-num new_line old" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC194" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>                                                            <span class="c1" style="color: #998; font-style: italic;">//  don't overlap</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uu</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">id</span><span class="p">())</span>   <span class="c1" style="color: #998; font-style: italic;">//  Skip if to a different tig.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

244

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>       <span class="c1" style="color: #998; font-style: italic;">//  (otherwise, ufpath[jj] is invalid below)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="diff-line-num new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

245

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

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<td class="diff-line-num new_line old" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC196" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Reads overlap.  Compute the position of the read using</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="diff-line-num new_line old" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC197" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  the overlap and the other read.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

246

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Compute the position of the read using the overlap and the other read.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<td class="diff-line-num new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

248

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">fwd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<td class="diff-line-num new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">fwd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">b_hang</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">jid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">a_hang</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

250

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

<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

203

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<td class="diff-line-num new_line old" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC203" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %8u olap %4u - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">oo</span><span class="p">,</span> <span class="n" style="color: #333;">tmin</span><span class="p">,</span> <span class="n" style="color: #333;">tmax</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %9u olap %4u - %9.2f-%-9.2f</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;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">oo</span><span class="p">,</span> <span class="n" style="color: #333;">tmin</span><span class="p">,</span> <span class="n" style="color: #333;">tmax</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

253

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Skip if the overlap isn't compatible with the layout.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

256

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">optimize_isCompatible</span><span class="p">(</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="p">,</span> <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">oo</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">beVerbose</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

257

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

258

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

<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Update estimate.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

204

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<td class="diff-line-num new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c">    <span class="n" style="color: #333;">nmin</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tmin</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

206

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<td class="diff-line-num new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

262

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

<pre style="margin: 0;"> <span id="LC262" class="line" lang="c">    <span class="n" style="color: #333;">nmax</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tmax</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

207

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<td class="diff-line-num new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

263

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

<pre style="margin: 0;"> <span id="LC263" class="line" lang="c">    <span class="n" style="color: #333;">cnt</span>  <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC208" class="line" lang="c">  <span class="p">}</span><span class="idiff left">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  over all overlaps</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

209

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<td class="diff-line-num new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

267

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

<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to optimize read %u in tig %u</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;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to optimize read %u in tig %u</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;">iid</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">());</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="c">    <span class="n" style="color: #333;">flushLog</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Add in some evidence for the bases in the read.  We want higher weight than the overlaps,</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">@@ -226,7 +287,7 @@ Unitig::optimize_recompute(uint32        iid,</td>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">dmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">npll</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %<span class="idiff left right">8</span>u           - %9.2f-%-9.2f length %9.2f/%-6d %7.2f%% posChange %+6.4f %+6.4f</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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<pre style="margin: 0;">+<span id="LC290" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- tig %8u read %<span class="idiff left right">9</span>u           - %9.2f-%-9.2f length %9.2f/%-6d %7.2f%% posChange %+6.4f %+6.4f</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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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c">             <span class="n" style="color: #333;">id</span><span class="p">(),</span> <span class="n" style="color: #333;">iid</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c">             <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c">             <span class="n" style="color: #333;">npll</span><span class="p">,</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); 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="298" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -237,8 +298,6 @@ Unitig::optimize_recompute(uint32        iid,</td>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"><span class="n" style="color: #333;">Unitig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">optimize_expand</span><span class="p">(</span><span class="n" style="color: #333;">optPos</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">op</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -300,7 +359,7 @@ Unitig::optimize_setPositions(optPos  *op,</td>

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<td class="diff-line-num old_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">fwd</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- read %<span class="idiff left right">8</span>u -> from %9d,%-9d %7d to %9d,%-9d %7d readLen %7d diff %7.4f%%</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="diff-line-num new old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- read %<span class="idiff left right">9</span>u -> from %9d,%-9d %7d to %9d,%-9d %7d readLen %7d diff %7.4f%%</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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<pre style="margin: 0;"> <span id="LC363" class="line" lang="c">                 <span class="n" style="color: #333;">iid</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="c">                 <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="c">                 <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,7 +374,7 @@ Unitig::optimize_setPositions(optPos  *op,</td>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="c">      <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">int32</span><span class="p">)</span><span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">iid</span><span class="p">].</span><span class="n" style="color: #333;">max</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC375" 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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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">beVerbose</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- read %<span class="idiff left right">8</span>u <- from %9d,%-9d %7d to %9d,%-9d %7d readLen %7d diff %7.4f%%</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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<pre style="margin: 0;">+<span id="LC377" class="line" lang="c">        <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize()-- read %<span class="idiff left right">9</span>u <- from %9d,%-9d %7d to %9d,%-9d %7d readLen %7d diff %7.4f%%</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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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c">                 <span class="n" style="color: #333;">iid</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c">                 <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">bgn</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c">                 <span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -358,14 +417,15 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c">  <span class="n" style="color: #333;">optPos</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">np</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">optPos</span> <span class="p">[</span><span class="n" style="color: #333;">fiLimit</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">pp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpathIdx</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>    <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>    <span class="n" style="color: #333;">pp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ufpathIdx</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>   <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC364" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ti</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ti<span class="idiff left">g</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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366

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426

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

367

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<td class="diff-line-num new_line old" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC367" class="line" lang="c">    <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">fi</span><span class="p">].</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">operator</span></span><span class="p"><span class="idiff">[](</span></span><span class="n" style="color: #333;"><span class="idiff">ti</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">pp</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

368

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<td class="diff-line-num new_line old" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC368" class="line" lang="c">    <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">fi</span><span class="p">].</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">operator</span></span><span class="p"><span class="idiff">[](</span></span><span class="n" style="color: #333;"><span class="idiff">ti</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">pp</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

427

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="c">    <span class="n" style="color: #333;">op</span><span class="p">[</span><span class="n" style="color: #333;">fi</span><span class="p">].</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">tig</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">pp</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

428

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="c">    <span class="n" style="color: #333;">np</span><span class="p">[</span><span class="n" style="color: #333;">fi</span><span class="p">].</span><span class="n" style="color: #333;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">tig</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="n" style="color: #333;">pp</span><span class="p">]);</span></span>

</pre>

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429

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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430

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Compute initial positions using previously placed reads and the read length.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -383,7 +443,7 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<td class="diff-line-num new_line" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="c">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">></span>   <span class="n" style="color: #333;">failed</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

445

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC386" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

446

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ufpath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

387

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<td class="diff-line-num new_line" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

447

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

448

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

<pre style="margin: 0;"> <span id="LC448" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -406,12 +466,13 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma omp parallel for schedule(dynamic, fiBlockSize)</span></span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">ti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="c">      <span class="n" style="color: #333;">Unitig</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC411" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">ti</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ufpath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="c">      <span class="n" style="color: #333;"><span class="idiff left">operator</span></span><span class="p"><span class="idiff">[](</span></span><span class="n" style="color: #333;"><span class="idiff">ti</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">optimize_recompute</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">,</span> <span class="n" style="color: #333;">beVerbose</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c">      <span class="n" style="color: #333;"><span class="idiff left right">tig</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">optimize_recompute</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">,</span> <span class="n" style="color: #333;">beVerbose</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="c"></span>

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417

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478

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Reset zero</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); 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="482" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -421,7 +482,7 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<td class="diff-line-num old_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

421

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<td class="diff-line-num new_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

422

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<td class="diff-line-num new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

483

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c">      <span class="n" style="color: #333;">Unitig</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

423

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<td class="diff-line-num new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

484

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

424

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<td class="diff-line-num new_line old" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC424" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

485

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ufpath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

425

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<td class="diff-line-num new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c">      <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">[</span> <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ident</span> <span class="p">].</span><span class="n" style="color: #333;">min</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); 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="540" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -479,7 +540,7 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<td class="diff-line-num old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

479

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<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

481

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<td class="diff-line-num new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

482

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<td class="diff-line-num new_line old" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC482" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ufpath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

483

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<td class="diff-line-num new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

484

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<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<td class="diff-line-num new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

546

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="c">    <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">optimize_expand</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); 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="555" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -494,7 +555,7 @@ TigVector::optimizePositions(const char *prefix, const char *label) {</td>

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<td class="diff-line-num old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<td class="diff-line-num new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tiLimit</span><span class="p">;</span> <span class="n" style="color: #333;">ti</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c">    <span class="n" style="color: #333;">Unitig</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">ti</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC497" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tig</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ufpath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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498

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<td class="diff-line-num new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<td class="diff-line-num new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c">    <span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">optimize_setPositions</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="n" style="color: #333;">beVerbose</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="80d80b4dca5a701d2ccaf42d170bdc564315dfe7">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#80d80b4dca5a701d2ccaf42d170bdc564315dfe7"><strong>src/bogart/AS_BAT_OverlapCache.C</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); 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="344" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -344,7 +344,7 @@ uint32</td>

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<td class="diff-line-num new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"><span class="n" style="color: #333;">OverlapCache</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filterDuplicates</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">no</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>   <span class="n" style="color: #333;">nFiltered</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">jj</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;">jj</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">no</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">no</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">jj</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC350" 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">@@ -352,22 +352,35 @@ OverlapCache::filterDuplicates(uint32 &no) {</td>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="c">    <span class="n" style="color: #333;">nFiltered</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Drop the <span class="idiff left right">shorter overlap, or the one with the higher erat</span>e.</span></span>

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Drop the <span class="idiff left right">weaker overlap.  If a tie, drop the flipped on</span>e.</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left">uint32</span></span><span class="idiff">  </span><span class="n" style="color: #333;"><span class="idiff">iilen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RI</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">overlapLength</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_hang</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_hang</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="c">    <span class="n" style="color: #333;"><span class="idiff left">uint32</span></span><span class="idiff">  </span><span class="n" style="color: #333;"><span class="idiff">jjlen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RI</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">overlapLength</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_hang</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_hang</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

357

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iiSco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RI</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">overlapLength</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_hang</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_hang</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">erate</span></span><span class="p"><span class="idiff right">(</span>);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

358

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jjSco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RI</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">overlapLength</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_hang</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_hang</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">erate</span></span><span class="p"><span class="idiff right">(</span>);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

359

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<td class="diff-line-num new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

359

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

360

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC360" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ii<span class="idiff left">len</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jjlen</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

361

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC361" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left">evalue</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">jj</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">evalue</span></span><span class="p"><span class="idiff right">())</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

362

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC362" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">jjlen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

363

</td>

<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC363" class="line" lang="c">      <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

364

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC364" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">iilen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

360

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

<pre style="margin: 0;">+<span id="LC360" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ii<span class="idiff left">Sco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jjSco</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff">             </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  Hey gcc!  See how nice I was by putting brackets</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

361

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

<pre style="margin: 0;">+<span id="LC361" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left">flipped</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff">         </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  around this so you don't get confused by the</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

362

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

<pre style="margin: 0;">+<span id="LC362" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">iiSco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff">                    </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  non-ambiguous ambiguous else clause?</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

363

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

<pre style="margin: 0;">+<span id="LC363" class="line" lang="c">      <span class="k" style="font-weight: 600;">else</span><span class="idiff left">                            </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c">        <span class="n" style="color: #333;"><span class="idiff left">jjSco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff">                    </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  You're welcome.</span></span></span>

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365

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="c">    <span class="p">}</span></span>

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366

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"></span>

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367

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ii<span class="idiff left">len</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">jjlen</span></span><span class="p">)</span></span>

</pre>

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368

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c">      <span class="n" style="color: #333;"><span class="idiff left">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">a_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_ovs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">b_iid</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ii<span class="idiff left">Sco</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">jjSco</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="c">      <span class="n" style="color: #333;"><span class="idiff left">dd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ii</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="c">      <span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">a_iid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">jj</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="c">      <span class="n" style="color: #333;">dd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">jj</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    writeLog("OverlapCache::filterDuplicates()-- Dropping overlap A: %9" F_U64P " B: %9" F_U64P " - %6.4f%% - %6" F_S32P " %6" F_S32P " - %s\n",</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].a_iid,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].b_iid,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].a_hang(),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].b_hang(),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].erate(),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">             _ovs[dd].flipped() ? "flipped" : "");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="c">    <span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">dd</span><span class="p">].</span><span class="n" style="color: #333;">a_iid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="c">    <span class="n" style="color: #333;">_ovs</span><span class="p">[</span><span class="n" style="color: #333;">dd</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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371

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

384

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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372

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385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

373

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<td class="diff-line-num new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

386

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If nothing was filtered, return.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); 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="629" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -616,30 +629,29 @@ OverlapCache::loadOverlaps(ovStore *ovlStore, bool doSave) {</td>

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616

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629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

617

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630

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Binary search a list of overlaps for one matching bID and flipped.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"><span class="n" style="color: #333;">bool</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC620" class="line" lang="c"><span class="n" style="color: #333;">searchForOverlap</span><span class="p">(</span><span class="n" style="color: #333;">BAToverlap</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ovl</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ovlLen</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="c"><span class="n" style="color: #333;">searchForOverlap</span><span class="p">(</span><span class="n" style="color: #333;">BAToverlap</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ovl</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ovlLen</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">bID</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">flipped</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ovlLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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637

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<td class="diff-line-num new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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

<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef TEST_LINEAR_SEARCH</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

</td>

<td class="diff-line-num new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="c">  <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">linearSearchFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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

<pre style="margin: 0;"> <span id="LC641" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<td class="diff-line-num new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ovlLen</span><span class="p">;</span> <span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

626

</td>

<td class="diff-line-num new_line old" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC626" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ss</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ss</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span>   <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

644

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="c">        <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">ss</span><span class="p">].</span><span class="n" style="color: #333;">flipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">flipped</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="diff-line-num new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

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

<pre style="margin: 0;"> <span id="LC645" class="line" lang="c">      <span class="n" style="color: #333;">linearSearchFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

</td>

<td class="diff-line-num new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

646

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

<pre style="margin: 0;"> <span id="LC646" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

</td>

<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

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

<pre style="margin: 0;"> <span id="LC647" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

</td>

<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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

<pre style="margin: 0;"> <span id="LC648" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

</td>

<td class="diff-line-num new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

649

</td>

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

<pre style="margin: 0;"> <span id="LC649" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

632

</td>

<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC632" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If not, these are repeats and we should binary search everything.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

633

</td>

<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC633" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  There will be no short lists where we could exhaustively search.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

634

</td>

<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC634" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

635

</td>

<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC635" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

636

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<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC636" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ovlLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>  <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC638" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">L</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="c">    <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">L</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC642" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span>   <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="c">        <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">flipped</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">flipped</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="c">      <span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">symmetric</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef TEST_LINEAR_SEARCH</span></span>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="c">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">linearSearchFound</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); 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="659" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -647,7 +659,8 @@ searchForOverlap(BAToverlap *ovl, uint32 ovlLen, uint32 bID) {</td>

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span>  <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bID</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="c">        <span class="p">((</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">ovl</span><span class="p">[</span><span class="n" style="color: #333;">M</span><span class="p">].</span><span class="n" style="color: #333;">flipped</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flipped</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

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<td class="diff-line-num new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

664

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c">      <span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

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<td class="diff-line-num new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

665

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c">    <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

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<td class="diff-line-num new_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

666

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

<pre style="margin: 0;"> <span id="LC666" class="line" lang="c">      <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); 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="707" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -694,7 +707,7 @@ OverlapCache::symmetrizeOverlaps(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

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<td class="diff-line-num new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="c"></span>

</pre>

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

695

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<td class="diff-line-num new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">//  Search for the twin overlap, and if found, we're done.  The twin is marked as symmetric in the function.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC697" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">searchForOverlap</span><span class="p">(</span><span class="n" style="color: #333;">_overlaps</span><span class="p">[</span><span class="n" style="color: #333;">rb</span><span class="p">],</span> <span class="n" style="color: #333;">_overlapLen</span><span class="p">[</span><span class="n" style="color: #333;">rb</span><span class="p">],</span> <span class="n" style="color: #333;">rr</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">searchForOverlap</span><span class="p">(</span><span class="n" style="color: #333;">_overlaps</span><span class="p">[</span><span class="n" style="color: #333;">rb</span><span class="p">],</span> <span class="n" style="color: #333;">_overlapLen</span><span class="p">[</span><span class="n" style="color: #333;">rb</span><span class="p">],</span> <span class="n" style="color: #333;">rr</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_overlaps</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">rr</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">oo</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">flipped</span></span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

698

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<td class="diff-line-num new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="c">        <span class="n" style="color: #333;">_overlaps</span><span class="p">[</span><span class="n" style="color: #333;">rr</span><span class="p">][</span><span class="n" style="color: #333;">oo</span><span class="p">].</span><span class="n" style="color: #333;">symmetric</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

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<td class="diff-line-num new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c">      <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="bdb859bee1536bade4d2c27e546c1ed397b0d93d">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#bdb859bee1536bade4d2c27e546c1ed397b0d93d"><strong>src/bogart/AS_BAT_PlaceContains.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,6 +65,11 @@ breakSingletonTigs(TigVector &tigs) {</td>

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65

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65

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

<pre style="margin: 0;"> <span id="LC65" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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

<pre style="margin: 0;"> <span id="LC66" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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

<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isZombie</span><span class="p">(</span><span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c">      <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"Not breaking sinleton zombie tig %u with read %u</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;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c">    <span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">ti</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span>                           <span class="c1" style="color: #998; font-style: italic;">//  Remove the tig from the list</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c">    <span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">registerRead</span><span class="p">(</span><span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ident</span><span class="p">);</span>   <span class="c1" style="color: #998; font-style: italic;">//  Eject the read</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c">    <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">utg</span><span class="p">;</span>                                <span class="c1" style="color: #998; font-style: italic;">//  Reclaim space</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="130" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -125,6 +130,16 @@ placeUnplacedUsingAllOverlaps(TigVector           &tigs,</td>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c">    <span class="n" style="color: #333;">placeReadUsingOverlaps</span><span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">fid</span><span class="p">,</span> <span class="n" style="color: #333;">placements</span><span class="p">,</span> <span class="n" style="color: #333;">placeRead_fullMatch</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  If all placements are in singletons, allow them.  If any placement is to a 'real' tig,</span></span>

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  ignore singleton placements.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c">    <span class="n" style="color: #333;">bool</span>  <span class="n" style="color: #333;">ignoreSingleton</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"></span>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">placements</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fCoverage</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">99</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c">          <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">tigID</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c">        <span class="n" style="color: #333;">ignoreSingleton</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"></span>

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Search the placements for the highest expected identity placement using all overlaps in the unitig.</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"></span>

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>   <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,10 +147,11 @@ placeUnplacedUsingAllOverlaps(TigVector           &tigs,</td>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">placements</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">      <span class="n" style="color: #333;">Unitig</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tigs</span><span class="p">[</span><span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">tigID</span><span class="p">];</span></span>

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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fCoverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">99</span><span class="p">)</span>     <span class="idiff left right">              </span><span class="c1" style="color: #998; font-style: italic;">//  Ignore partially placed reads.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fCoverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">99</span><span class="p">)</span>     <span class="c1" style="color: #998; font-style: italic;">//  Ignore partially placed reads.</span></span>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC138" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;">//  Ignore placements in singletons.</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ignoreSingleton</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

154

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c">          <span class="p">(</span><span class="n" style="color: #333;">tig</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span>          <span class="c1" style="color: #998; font-style: italic;">//  Ignore placements in singletons.</span></span>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c">      <span class="n" style="color: #333;">uint32</span>  <span class="n" style="color: #333;">bgn</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">placements</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">position</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">();</span></span>

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<br>

</li>

<li id="afe103f609fd2a6e84ded26153c9411bd4265e9f">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#afe103f609fd2a6e84ded26153c9411bd4265e9f"><strong>src/bogart/AS_BAT_PopulateUnitig.C</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); 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="119" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -119,8 +119,11 @@ populateUnitig(TigVector &tigs,</td>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">               <span class="n" style="color: #333;">int32</span>      <span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">RI</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readLength</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span>      <span class="c1" style="color: #998; font-style: italic;">//  Skip deleted</span></span>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span>         <span class="c1" style="color: #998; font-style: italic;">//  Skip placed</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isContained</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">))</span>    <span class="c1" style="color: #998; font-style: italic;">//  Skip contained</span></span>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">inUnitig</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span>         <span class="c1" style="color: #998; font-style: italic;">//  Skip placed</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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

<pre style="margin: 0;">+<span id="LC125" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isContained</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span>  <span class="c1" style="color: #998; font-style: italic;">//  Skip contained...</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isZombie</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">))</span>      <span class="c1" style="color: #998; font-style: italic;">//  that aren't zombies.</span></span>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"></span>

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126

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c">  <span class="n" style="color: #333;">Unitig</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tigs</span><span class="p">.</span><span class="n" style="color: #333;">newUnitig</span><span class="p">(</span><span class="n" style="color: #333;">logFileFlagSet</span><span class="p">(</span><span class="n" style="color: #333;">LOG_BUILD_UNITIG</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -140,6 +143,22 @@ populateUnitig(TigVector &tigs,</td>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c">  <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addRead</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">logFileFlagSet</span><span class="p">(</span><span class="n" style="color: #333;">LOG_BUILD_UNITIG</span><span class="p">));</span></span>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If suspicious or a zombie, don't bother trying to extend.  In the former</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  case, we don't want to extend, and in the latter case, there isn't anything</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  to extend.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSuspicious</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"Stopping unitig construction of suspicious read %d in unitig %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="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c">            <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">ident</span><span class="p">,</span> <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isZombie</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"Stopping unitig construction of zombie read %d in unitig %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c">            <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">ident</span><span class="p">,</span> <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c">  <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Add reads as long as there is a path to follow...from the 3' end of the first read.</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c">  <span class="n" style="color: #333;">BestEdgeOverlap</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestedge5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getBestEdgeOverlap</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -150,34 +169,6 @@ populateUnitig(TigVector &tigs,</td>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bestedge3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ahang</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bestedge3</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bhang</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC153" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If this read is not covered by the two best overlaps we are finished.  We will not follow</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  the paths out.  This indicates either low coverage, or a chimeric read.  If it is low</span></span>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC155" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  coverage, then the best overlaps will be mutual and we'll recover the same path.  If it is a</span></span>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC156" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  chimeric read the overlaps will not be mutual and we will skip this read.</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC158" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  The amount of our read that is covered by the two best overlaps is</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//    (readLen + bestedge5->bhang()) + (readLen - bestedge3->ahang())</span></span>

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161

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If that is not significantly longer than the read length, then we will not use this</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC163" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  read as a seed for unitig construction.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC164" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC165" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC166" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OG</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSuspicious</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">))</span></span>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC167" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC168" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

169

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC169" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

170

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  uint32  covered = RI->readLength(fi) + bestedge5->bhang() + RI->readLength(fi) - bestedge3->ahang();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC171" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC172" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  //  This breaks tigs at 0x best-coverage regions.  There might be a contain that spans (joins)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

173

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC173" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  //  the two best overlaps to verify the read, but we can't easily tell right now.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC174" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  if (covered < RI->readLength(fi) + AS_OVERLAP_MIN_LEN / 2) {</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

175

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC175" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    writeLog("Stopping unitig construction of suspicious read %d in unitig %d\n",</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC176" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">            utg->ufpath.back().ident, utg->id());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

177

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">    return;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

178

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC178" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">  }</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">logFileFlagSet</span><span class="p">(</span><span class="n" style="color: #333;">LOG_BUILD_UNITIG</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c">    <span class="n" style="color: #333;">writeLog</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding 5' edges off of read %d in unitig %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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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">            <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ufpath</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">ident</span><span class="p">,</span> <span class="n" style="color: #333;">utg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">());</span></span>

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<br>

</li>

<li id="bd441caac58d9b73f15ae842113848828869ce32">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#bd441caac58d9b73f15ae842113848828869ce32"><strong>src/bogart/AS_BAT_Unitig.H</strong></a>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "AS_global.H"</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "AS_BAT_TigVector.H"</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "AS_BAT_OverlapCache.H"</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stddev.H"</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">cleanUp</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Recompute bgn/end positions using all overlaps.</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c">  <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">optimize_isCompatible</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span>       <span class="n" style="color: #333;">ii</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="c">                             <span class="n" style="color: #333;">uint32</span>       <span class="n" style="color: #333;">jj</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c">                             <span class="n" style="color: #333;">BAToverlap</span>  <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">olap</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c">                             <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">inInit</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c">                             <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">secondPass</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c">                             <span class="n" style="color: #333;">bool</span>         <span class="n" style="color: #333;">beVerbose</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">optimize_initPlace</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">pp</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c">                          <span class="n" style="color: #333;">optPos</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">op</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c">                          <span class="n" style="color: #333;">optPos</span>       <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">np</span><span class="p">,</span></span>

</pre>

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<br>

</li>

<li id="785523ef798e0c6ec8990d8bf4a76216dbc5f373">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#785523ef798e0c6ec8990d8bf4a76216dbc5f373"><strong>src/canu_version_update.pl</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +32,7 @@ my $cwd = getcwd();</td>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$label</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"snapshot"</span><span class="p">;</span>     <span class="c1" style="color: #998; font-style: italic;">#  Automagically set to 'release' for releases.</span></span>

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$major</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span>            <span class="c1" style="color: #998; font-style: italic;">#  Bump before release.</span></span>

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

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<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC35" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$minor</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"7<span class="idiff left">"</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right">  </span>          <span class="c1" style="color: #998; font-style: italic;">#  Bump before release.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$minor</span>    <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"7<span class="idiff left">.1"</span></span><span class="p"><span class="idiff right">;</span></span>          <span class="c1" style="color: #998; font-style: italic;">#  Bump before release.</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$commits</span>  <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$hash1</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">;</span>          <span class="c1" style="color: #998; font-style: italic;">#  This from 'git describe'</span></span>

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</li>

<li id="37f197c29a6f3776ccaf400a51d8efdfbb79af21">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#37f197c29a6f3776ccaf400a51d8efdfbb79af21"><strong>src/overlapErrorAdjustment/findErrors-Read_Frags.C</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,9 +60,6 @@ Read_Frags(feParameters   *G,</td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span>  <span class="n" style="color: #333;">votesLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span>  <span class="n" style="color: #333;">readsLoaded</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Frags()-- from "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" through "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">"</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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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c">          <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgnID</span><span class="p">,</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">endID</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">curID</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgnID</span><span class="p">;</span> <span class="n" style="color: #333;">curID</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">endID</span><span class="p">;</span> <span class="n" style="color: #333;">curID</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c">    <span class="n" style="color: #333;">gkRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_getRead</span><span class="p">(</span><span class="n" style="color: #333;">curID</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,11 +71,7 @@ Read_Frags(feParameters   *G,</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c">                      <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Vote_Tally_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">votesLength</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c">                      <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Frag_Info_t</span><span class="p">)</span>  <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Frags()-- allocate "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" MB for bases, votes and info, for %u reads of total length "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" (%.2f MB)</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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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c">          <span class="n" style="color: #333;">totAlloc</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">20</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c">          <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">endID</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgnID</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="c">          <span class="n" style="color: #333;">basesLength</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c">          <span class="n" style="color: #333;">totAlloc</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Frags()-- Loading target reads "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" through "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" with "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" bases.</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;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bgnID</span><span class="p">,</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">endID</span><span class="p">,</span> <span class="n" style="color: #333;">basesLength</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c">  <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span>          <span class="p">[</span><span class="n" style="color: #333;">basesLength</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c">  <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readVotes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">Vote_Tally_t</span>  <span class="p">[</span><span class="n" style="color: #333;">votesLength</span><span class="p">];</span>             <span class="c1" style="color: #998; font-style: italic;">//  NO constructor, MUST INIT</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); 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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -122,6 +115,6 @@ Read_Frags(feParameters   *G,</td>

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115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c">  <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">readData</span><span class="p">;</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Frags()-- <span class="idiff left">from "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U32</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" through "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U32</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" -- loaded "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U64</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" bases in "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U64</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" reads.</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

126

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<td class="diff-line-num new_line old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC126" class="line" lang="c">  <span class="idiff left">        </span><span class="n" style="color: #333;"><span class="idiff">G</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">bgnID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">G</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">endID</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">basesLength</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">readsLoaded</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Frags()-- <span class="idiff left">%.3f GB for bases, votes and info.</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">totAlloc</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<br>

</li>

<li id="b94ee93cab4ade098360f99895c9e7b4ff7bd114">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#b94ee93cab4ade098360f99895c9e7b4ff7bd114"><strong>src/overlapErrorAdjustment/findErrors-Read_Olaps.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); 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="41" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -41,8 +41,7 @@ Read_Olaps(feParameters *G, gkStore *gkpStore) {</td>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">numolaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ovs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numOverlapsInRange</span><span class="p">();</span></span>

</pre>

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43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"></span>

</pre>

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44

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC44" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Olaps()-- loading "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" overlaps (%.2f MB).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC45" class="line" lang="c">          <span class="n" style="color: #333;">numolaps</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Olap_Info_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numolaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Olaps()-- Loading "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" overlaps.</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;">numolaps</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c">  <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">Olap_Info_t</span> <span class="p">[</span><span class="n" style="color: #333;">numolaps</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">  <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); 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="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,6 +67,9 @@ Read_Olaps(feParameters *G, gkStore *gkpStore) {</td>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c">  <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">ovs</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Read_Olaps()-- %.3f GB for overlaps..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Olap_Info_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numolaps</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1024</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>

</pre>

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<li id="e16a09a812c43c51f5e5e85e9236de450fa6be09">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#e16a09a812c43c51f5e5e85e9236de450fa6be09"><strong>src/overlapErrorAdjustment/findErrors.C</strong></a>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  From overlapInCore.C</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="n" style="color: #333;">Binomial_Bound</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Start</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Limit</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Read fragments lo_frag..hi_frag (INCLUSIVE) from store and save the ids and sequences of those</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  with overlaps to fragments in global Frag .</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Extract_Needed_Frags</span><span class="p">(</span><span class="n" style="color: #333;">feParameters</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">G</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="c">                     <span class="n" style="color: #333;">gkStore</span>      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gkpStore</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c">                     <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">loID</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="c">                     <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">hiID</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c">                     <span class="n" style="color: #333;">Frag_List_t</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fl</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c">                     <span class="n" style="color: #333;">uint64</span>       <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nextOlap</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">extractReads</span><span class="p">(</span><span class="n" style="color: #333;">feParameters</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">G</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c">             <span class="n" style="color: #333;">gkStore</span>      <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gkpStore</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c">             <span class="n" style="color: #333;">Frag_List_t</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fl</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c">             <span class="n" style="color: #333;">uint64</span>       <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nextOlap</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Clear the buffer.</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  The original converted to lowercase, and made non-acgt be 'a'.</span></span>

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<pre style="margin: 0;"> <span id="LC70" 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">@@ -81,35 +78,44 @@ Extract_Needed_Frags(feParameters *G,</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c">  <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="sc" style="color: #d14;">'G'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="sc" style="color: #d14;">'g'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c">  <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="sc" style="color: #d14;">'T'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="sc" style="color: #d14;">'t'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="c"> <span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  Count the amount of stuff we're loading</span>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  Return if we've exhausted the overlaps</span>.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

86

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<td class="diff-line-num new_line old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

87

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<td class="diff-line-num new_line old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC87" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Count the amount of stuff we're loading.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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

<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">lastOlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span>       <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>                        <span class="c1" style="color: #998; font-style: italic;">//  Index into reads arrays</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">fi</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">//  Actual ID we're extracting</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">loID</span>     <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">//  Actual ID we're extracting</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">hiID</span>     <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loID</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">maxBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC93" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">assert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">loID</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fi</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  Find the highest read ID that we can load without exceeding maxBases.</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC95" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC96" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extract_Needed_Frags()--  Loading used reads between "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" and "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">", at overlap "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">".</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;">fi</span><span class="p">,</span> <span class="n" style="color: #333;">hiID</span><span class="p">,</span> <span class="n" style="color: #333;">lastOlap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxBases</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">         <span class="p">(</span><span class="n" style="color: #333;">lastOlap</span>     <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c">    <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span>                        <span class="c1" style="color: #998; font-style: italic;">//  Grab the ID of the overlap we're at.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC98" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hiID</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC99" class="line" lang="c">    <span class="n" style="color: #333;">gkRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_getRead</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c">    <span class="n" style="color: #333;">gkRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_getRead</span><span class="p">(</span><span class="n" style="color: #333;">hiID</span><span class="p">);</span>         <span class="c1" style="color: #998; font-style: italic;">//  Grab that read.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC101" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="idiff left">                                      </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  Add the read to our set.</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkRead_sequenceLength</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC104" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Advance to the next overlap</span></span>

</pre>

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105

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="c"></span>

</pre>

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106

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="c">    <span class="n" style="color: #333;">lastOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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107

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">lastOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fi</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

108

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="c">      <span class="n" style="color: #333;">lastOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

109

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="c">    <span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lastOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c">   <span class="n" style="color: #333;">lastOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span>                                             <span class="c1" style="color: #998; font-style: italic;">//  Advance to the next overlap</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">lastOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span>                      <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c">           <span class="p">(</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">lastOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hiID</span><span class="p">))</span>              <span class="c1" style="color: #998; font-style: italic;">//  If we've exceeded the max size or hit the last overlap,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c">      <span class="n" style="color: #333;">lastOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span>                                           <span class="c1" style="color: #998; font-style: italic;">//  the loop will stop on the next iteration.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC112" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extract_Needed_Frags()--  Loading reads for overlaps "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" to "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" (reads "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" bases "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">")</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;">nextOlap</span><span class="p">,</span> <span class="n" style="color: #333;">lastOlap</span><span class="p">,</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">,</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If nothing to load, just return.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Report what we're going to do.</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"extractReads()-- Loading reads "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" to "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" ("</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" reads with "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" bases) overlaps "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" through "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">".</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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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c">          <span class="n" style="color: #333;">loID</span><span class="p">,</span> <span class="n" style="color: #333;">hiID</span><span class="p">,</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">,</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span><span class="p">,</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">,</span> <span class="n" style="color: #333;">lastOlap</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Ensure there is space.</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,42 +123,31 @@ Extract_Needed_Frags(feParameters *G,</td>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c">    <span class="n" style="color: #333;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c">    <span class="n" style="color: #333;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "Extract_Needed_Frags()--  realloc reads from " F_U32 " to " F_U32 "\n", fl->readsMax, 12 * fl->readsLen / 10);</span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">uint32</span> <span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsMax</span>  <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">uint32</span> <span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsMax</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsMax</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesMax</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">    <span class="n" style="color: #333;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bases</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "Extract_Needed_Frags()--  realloc bases from " F_U64 " to " F_U64 "\n", fl->basesMax, 12 * fl->basesLen / 10);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bases</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesMax</span>    <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bases</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesMax</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

136

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Load.  This is complicated by loading only the reads that have overlaps we care about.</span></span>

</pre>

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139

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC139" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC140" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="diff-line-num new_line old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC141" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Load the sequence data for reads loID to hiID, as long as the read has an overlap.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c">  <span class="n" style="color: #333;">gkReadData</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">gkReadData</span><span class="p">;</span></span>

</pre>

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

144

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC145" class="line" lang="c">  <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

146

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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC146" class="line" lang="c">  <span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">nextOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

147

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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c">  <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hiID</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

151

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<td class="diff-line-num new_line old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c">    <span class="n" style="color: #333;">gkRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_getRead</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hiID</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c">         <span class="p">(</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c">    <span class="n" style="color: #333;">gkRead</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span>       <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_getRead</span><span class="p">(</span><span class="n" style="color: #333;">loID</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"></span>

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<td class="diff-line-num new_line old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span>     <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fi</span><span class="p">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span>       <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkRead_sequenceLength</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span><span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">]</span>   <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loID</span><span class="p">;</span>                          <span class="c1" style="color: #998; font-style: italic;">//  Save the ID of _this_ read.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span><span class="p">;</span>      <span class="c1" style="color: #998; font-style: italic;">//  Set the data pointer to where this read should start.</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">    <span class="n" style="color: #333;">gkpStore</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkStore_loadReadData</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">readData</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,31 +155,25 @@ Extract_Needed_Frags(feParameters *G,</td>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">char</span>   <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readBases</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readData</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkReadData_getSequence</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">readLen</span><span class="p">;</span> <span class="n" style="color: #333;">bb</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="c">      <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">ii</span></span><span class="p">][</span><span class="n" style="color: #333;">bb</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;">bb</span><span class="p">]];</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c">      <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">fl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">readsLen</span></span><span class="p">][</span><span class="n" style="color: #333;">bb</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter</span><span class="p">[</span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;">bb</span><span class="p">]];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC165" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">ii</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">readLen</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span>  <span class="c1" style="color: #998; font-style: italic;">//  All good reads end.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readBases</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">fl</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">readsLen</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">readLen</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right">                  </span>  <span class="c1" style="color: #998; font-style: italic;">//  All good reads end.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<td class="diff-line-num new_line old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC167" class="line" lang="c">    <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">basesLen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gkRead_sequenceLength</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>           <span class="c1" style="color: #998; font-style: italic;">//  Update basesLen to account for this read.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c">    <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>                                           <span class="c1" style="color: #998; font-style: italic;">//  And note that we loaded a read.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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

<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Advance to the next overlap.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c">    <span class="n" style="color: #333;">nextOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">nextOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">fi</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c">    <span class="n" style="color: #333;">nextOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span>                                                  <span class="c1" style="color: #998; font-style: italic;">//  Advance past all the overlaps for this read.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">    <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c">           <span class="p">(</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">nextOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">loID</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c">      <span class="n" style="color: #333;">nextOlap</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="diff-line-num new_line old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC174" class="line" lang="c">    <span class="n" style="color: #333;">fi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">nextOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</span><span class="p">)</span>                                  <span class="c1" style="color: #998; font-style: italic;">//  If we have valid overlap, grab the read ID.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c">      <span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">nextOlap</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span>                           <span class="c1" style="color: #998; font-style: italic;">//  If we don't have a valid overlap, the loop will stop.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c">  <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">readData</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" class="line" lang="c">  <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ii</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC180" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC181" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

182

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extract_Needed_Frags()--  Loaded "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" reads (%.4f%%).  Loaded IDs "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" through "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC183" class="line" lang="c">            <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">loID</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="c">            <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readIDs</span><span class="p">[</span><span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC185" class="line" lang="c">  <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC186" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Extract_Needed_Frags()--  Loaded "</span> <span class="n" style="color: #333;">F_U32</span> <span class="s" style="color: #d14;">" reads (%.4f%%).</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC187" class="line" lang="c">            <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readsLen</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">loID</span><span class="p">));</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"extractReads()-- Loaded.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -262,8 +251,6 @@ Threaded_Stream_Old_Frags(feParameters *G,</td>

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<td class="diff-line-num old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numThreads</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">thread_id</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC265" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">loID</span>         <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC266" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">hiID</span>         <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

254

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">nextOlap</span>     <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">G</span>            <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">frag_list</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -278,14 +265,6 @@ Threaded_Stream_Old_Frags(feParameters *G,</td>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c">    <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ped</span><span class="p">.</span><span class="n" style="color: #333;">initialize</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">,</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">errorRate</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">loID</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">b_iid</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">hiID</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">FRAGS_PER_BATCH</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"></span>

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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">endID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olaps</span><span class="p">[</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">olapsLen</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;">b_iid</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">endID</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="c">    <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endID</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">frstOlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">nextOlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -295,15 +274,13 @@ Threaded_Stream_Old_Frags(feParameters *G,</td>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c">  <span class="n" style="color: #333;">Frag_List_t</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">curr_frag_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">frag_list_1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c">  <span class="n" style="color: #333;">Frag_List_t</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next_frag_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">frag_list_2</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">Extract_Needed_Frags</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">G</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gkpStore</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">loID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">hiID</span></span><span class="p">,</span> <span class="n" style="color: #333;">curr_frag_list</span><span class="p">,</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">extractReads</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">G</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">gkpStore</span></span><span class="p">,</span> <span class="n" style="color: #333;">curr_frag_list</span><span class="p">,</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">loID</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">endID</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">curr_frag_list</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">readsLen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Process fragments in curr_frag_list in background</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numThreads</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c">      <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">loID</span>      <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loID</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c">      <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">hiID</span>      <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiID</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c">      <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">nextOlap</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frstOlap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c">      <span class="n" style="color: #333;">thread_wa</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">frag_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">curr_frag_list</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -315,21 +292,14 @@ Threaded_Stream_Old_Frags(feParameters *G,</td>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Read next batch of fragments</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC318" class="line" lang="c">    <span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC319" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

320

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<td class="diff-line-num new_line old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC320" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">endID</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

321

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<td class="diff-line-num new_line old" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC321" class="line" lang="c">      <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loID</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">FRAGS_PER_BATCH</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

295

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c">    <span class="n" style="color: #333;">frstOlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

322

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<td class="diff-line-num new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

296

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

<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

323

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">endID</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

324

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="c">        <span class="n" style="color: #333;">hiID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endID</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

325

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

326

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="c">      <span class="n" style="color: #333;">frstOlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

327

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC327" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

328

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="c">      <span class="n" style="color: #333;">Extract_Needed_Frags</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">,</span> <span class="n" style="color: #333;">gkpStore</span><span class="p">,</span> <span class="n" style="color: #333;">loID</span><span class="p">,</span> <span class="n" style="color: #333;">hiID</span><span class="p">,</span> <span class="n" style="color: #333;">next_frag_list</span><span class="p">,</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

329

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<td class="diff-line-num new_line old" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

297

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c">    <span class="n" style="color: #333;">extractReads</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">,</span> <span class="n" style="color: #333;">gkpStore</span><span class="p">,</span> <span class="n" style="color: #333;">next_frag_list</span><span class="p">,</span> <span class="n" style="color: #333;">nextOlap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

330

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<td class="diff-line-num new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

298

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

<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

331

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<td class="diff-line-num new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

299

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Wait for background processing to finish</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

301

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"processReads()-- Waiting for compute.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

333

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<td class="diff-line-num new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numThreads</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c">      <span class="kt" style="color: #458; font-weight: 600;">void</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"></span>

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</li>

<li id="f6e23366bcce102996f2e38e40ac18feb1f78723">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#f6e23366bcce102996f2e38e40ac18feb1f78723"><strong>src/overlapErrorAdjustment/findErrors.H</strong></a>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Factor by which to grow memory in olap array when reading it</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define  EXPANSION_FACTOR            1.4</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Number of old fragments to read into memory-based fragment</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  store at a time for processing</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define  FRAGS_PER_BATCH             100000</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//  Longest name allowed for a file in the overlap store</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define  MAX_FILENAME_LEN            1000</span></span>

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

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Thread_Work_Area_t</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c">  <span class="n" style="color: #333;">int32</span>         <span class="n" style="color: #333;">thread_id</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">loID</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">hiID</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span>        <span class="n" style="color: #333;">nextOlap</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

280

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<td class="diff-line-num new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c">  <span class="n" style="color: #333;">feParameters</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">G</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="5968ef8e04a03bc22f685551138c5e796da880c0">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#5968ef8e04a03bc22f685551138c5e796da880c0"><strong>src/pipelines/canu/Defaults.pm</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); 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="682" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -682,7 +682,7 @@ sub setOverlapDefaults ($$$) {</td>

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<td class="diff-line-num old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

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682

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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<td class="diff-line-num new_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlHashBlockLength"</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">undef</span><span class="p">,</span>                     <span class="s" style="color: #d14;">"Amount of sequence (bp) to load into the overlap hash table"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

684

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<td class="diff-line-num new_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC684" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlRefBlockLength"</span><span class="p">,</span>   <span class="nb" style="color: #0086b3;">undef</span><span class="p">,</span>                     <span class="s" style="color: #d14;">"Amount of sequence (bp) to search against the hash table per batch"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

685

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<td class="diff-line-num new_line old" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC685" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlHashBits"</span><span class="p">,</span>         <span class="p"><span class="idiff left">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$tag</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"cor"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">?</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">18</span></span><span class="idiff"> </span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">23</span></span><span class="p"><span class="idiff right">,</span></span> <span class="s" style="color: #d14;">"Width of the kmer hash.  Width 22=1gb, 23=2gb, 24=4gb, 25=8gb.  Plus 10b per ${tag}OvlHashBlockLength"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

685

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlHashBits"</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;"><span class="idiff left">undef</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right">                    </span> <span class="s" style="color: #d14;">"Width of the kmer hash.  Width 22=1gb, 23=2gb, 24=4gb, 25=8gb.  Plus 10b per ${tag}OvlHashBlockLength"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

686

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<td class="diff-line-num new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

686

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlHashLoad"</span><span class="p">,</span>         <span class="mf" style="color: #099;">0.75</span><span class="p">,</span>                      <span class="s" style="color: #d14;">"Maximum hash table load.  If set too high, table lookups are inefficent; if too low, search overhead dominates run time; default 0.75"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

687

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<td class="diff-line-num new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

687

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlMerSize"</span><span class="p">,</span>          <span class="p">(</span><span class="nv" style="color: teal;">$tag</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"cor"</span><span class="p">)</span> <span class="p">?</span> <span class="mi" style="color: #099;">19</span> <span class="p">:</span> <span class="mi" style="color: #099;">22</span><span class="p">,</span> <span class="s" style="color: #d14;">"K-mer size for seeds in overlaps"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

688

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="perl">    <span class="nv" style="color: teal;">setOverlapDefault</span><span class="p">(</span><span class="nv" style="color: teal;">$tag</span><span class="p">,</span> <span class="s" style="color: #d14;">"OvlMerThreshold"</span><span class="p">,</span>     <span class="s" style="color: #d14;">"auto"</span><span class="p">,</span>                    <span class="s" style="color: #d14;">"K-mer frequency threshold; mers more frequent than this count are ignored; default 'auto'"</span><span class="p">);</span></span>

</pre>

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</li>

<li id="6a1192e790904d7df30212037b58266d09e0eace">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#6a1192e790904d7df30212037b58266d09e0eace"><strong>src/pipelines/canu/OverlapErrorAdjustment.pm</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,9 +58,13 @@ use canu::Grid_Cloud;</td>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">loadReadLengthsAndNumberOfOverlaps</span> <span class="p">($$$$)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$asm</span>     <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxID</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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61

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rlVec</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rlCnt</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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62

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

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rlSum</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"></span>

</pre>

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

63

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$noVec</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$noCnt</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$noSum</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$bin</span>     <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getBinDirectory</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,13 +79,19 @@ sub loadReadLengthsAndNumberOfOverlaps ($$$$) {</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: teal;">F</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="perl">        <span class="sr" style="color: #009926;">s/^\s+//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="perl">        <span class="sr" style="color: #009926;">s/\s+$//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl">        <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="sr" style="color: #009926;">m/^readID/</span><span class="p">);</span>   <span class="c1" style="color: #998; font-style: italic;">#  Header line</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl">        <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="sr" style="color: #009926;">m/^------/</span><span class="p">);</span>   <span class="c1" style="color: #998; font-style: italic;">#  ------ ----</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@v</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="s" style="color: #d14;">'\s+'</span><span class="p">,</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">vec</span><span class="p">(</span><span class="nv" style="color: teal;">$$rlVec</span><span class="p">,</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="perl">        <span class="nv" style="color: teal;">$rlCnt</span>                 <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="perl">        <span class="nv" style="color: teal;">$rlSum</span>                 <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">F</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC84" class="line" lang="perl">    <span class="nv" style="color: teal;">caExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to load read lengths from '$asm.gkpStore'"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span>   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$rl<span class="idiff left right">Sum</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="perl">    <span class="nv" style="color: teal;">caExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to load read lengths from '$asm.gkpStore'"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span>   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$rl<span class="idiff left right">Cnt</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl">    <span class="nv" style="color: teal;">fetchStore</span><span class="p">(</span><span class="s" style="color: #d14;">"unitigging/$asm.ovlStore"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); 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="102" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -92,13 +102,16 @@ sub loadReadLengthsAndNumberOfOverlaps ($$$$) {</td>

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: teal;">F</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl">        <span class="sr" style="color: #009926;">s/^\s+//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl">        <span class="sr" style="color: #009926;">s/\s+$//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@v</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span> <span class="s" style="color: #d14;">'\s+'</span><span class="p">,</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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

<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">vec</span><span class="p">(</span><span class="nv" style="color: teal;">$$noVec</span><span class="p">,</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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

<pre style="margin: 0;">+<span id="LC109" class="line" lang="perl">        <span class="nv" style="color: teal;">$noCnt</span>                 <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

</td>

<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl">        <span class="nv" style="color: teal;">$noSum</span>                 <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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

<pre style="margin: 0;"> <span id="LC111" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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

<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">F</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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

<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

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<td class="diff-line-num new_line old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC101" class="line" lang="perl">    <span class="nv" style="color: teal;">caExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to load number of overlaps per read from '$asm.ovlStore'"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span>   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$no<span class="idiff left right">Sum</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl">    <span class="nv" style="color: teal;">caExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to load number of overlaps per read from '$asm.ovlStore'"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span>   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$no<span class="idiff left right">Cnt</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

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

<pre style="margin: 0;"> <span id="LC115" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl">    <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="nv" style="color: teal;">$rlSum</span><span class="p">,</span> <span class="nv" style="color: teal;">$noSum</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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

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

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,25 +140,24 @@ sub readErrorDetectionConfigure ($) {</td>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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

<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$rlVec</span><span class="p">,</span> <span class="nv" style="color: teal;">$noVec</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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

<pre style="margin: 0;"> <span id="LC141" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$rlSum</span><span class="p">,</span> <span class="nv" style="color: teal;">$noSum</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">loadReadLengthsAndNumberOfOverlaps</span><span class="p">(</span><span class="nv" style="color: teal;">$asm</span><span class="p">,</span> <span class="nv" style="color: teal;">$maxID</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$rlVec</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">$noVec</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

129

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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

<pre style="margin: 0;"> <span id="LC142" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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

<pre style="margin: 0;">+<span id="LC143" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$noSum</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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

<pre style="margin: 0;">+<span id="LC144" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"--\n"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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

<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"-- WARNING:\n"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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

<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"-- WARNING: Found no overlaps.  Disabling Overlap Error Adjustment.\n"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

147

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

<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"-- WARNING:\n"</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

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

<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"--\n"</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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

<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl">        <span class="nv" style="color: teal;">setGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"enableOEA"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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

<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl">        <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

</td>

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

<pre style="margin: 0;">+<span id="LC151" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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

<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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

<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;">#  Find the maximum size of each block of 100,000 reads.  findErrors reads up to 100,000 reads</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

131

</td>

<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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

<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;">#  to process at one time.  It uses 1 * length + 4 * 100,000 bytes of memory for bases and ID storage,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

</td>

<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

</td>

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

<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;">#  and has two buffers of this size.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

</td>

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

<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC134" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxBlockSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC136" class="line" lang="perl">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nv" style="color: teal;">$maxID</span><span class="p">;</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">100000</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

137

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC137" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

138

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC138" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC139" class="line" lang="perl">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ii</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$id</span><span class="p">;</span> <span class="p">(</span><span class="nv" style="color: teal;">$ii</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">100000</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$ii</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$maxID</span><span class="p">);</span> <span class="nv" style="color: teal;">$ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC140" class="line" lang="perl">            <span class="nv" style="color: teal;">$sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">vec</span><span class="p">(</span><span class="nv" style="color: teal;">$rlVec</span><span class="p">,</span> <span class="nv" style="color: teal;">$ii</span><span class="p">,</span> <span class="mi" style="color: #099;">32</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC141" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC142" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC143" class="line" lang="perl">        <span class="nv" style="color: teal;">$maxBlockSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$sum</span>   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$maxBlockSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$sum</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC144" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC145" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

146

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC146" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxMem</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redMemory"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

147

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redBatchSize"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

148

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<td class="diff-line-num new_line old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redBatchLength"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxBlockSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">#  This is hardcoded in findErrors.C</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

158

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

<pre style="margin: 0;">+<span id="LC158" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxMem</span>       <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redMemory"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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

<pre style="margin: 0;">+<span id="LC159" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxReads</span>     <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redBatchSize"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

160

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

<pre style="margin: 0;">+<span id="LC160" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxBases</span>     <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redBatchLength"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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

<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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

<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"--\n"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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

<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"-- Configure RED for "</span><span class="p">,</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"redMemory"</span><span class="p">),</span> <span class="s" style="color: #d14;">"gb memory.\n"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -426,9 +438,6 @@ sub overlapErrorAdjustmentConfigure ($) {</td>

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<td class="diff-line-num new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

438

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

<pre style="margin: 0;"> <span id="LC438" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

427

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<td class="diff-line-num new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

439

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

<pre style="margin: 0;"> <span id="LC439" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

428

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<td class="diff-line-num new_line" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

440

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

<pre style="margin: 0;"> <span id="LC440" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

429

</td>

<td class="diff-line-num new_line old" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC429" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># get earliest count of reads in store</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

430

</td>

<td class="diff-line-num new_line old" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC430" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxID</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getNumberOfReadsEarliestVersion</span><span class="p">(</span><span class="nv" style="color: teal;">$asm</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

431

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<td class="diff-line-num new_line old" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC431" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC441" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxMem</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"oeaMemory"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

433

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<td class="diff-line-num new_line" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

442

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

<pre style="margin: 0;"> <span id="LC442" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"oeaBatchSize"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC443" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$maxBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">getGlobal</span><span class="p">(</span><span class="s" style="color: #d14;">"oeaBatchLength"</span><span class="p">);</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="23da18f1c1a1c22da72b64d5a004a6dd361e2681">

<a href="https://salsa.debian.org/med-team/canu/compare/af4642f176e567ccc5afe860c278c0b4d401bac2...b0bd43c00403591d5484a22a0d23e960204e8fad#23da18f1c1a1c22da72b64d5a004a6dd361e2681"><strong>src/stores/ovStore.C</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +54,11 @@</td>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"></span>

</pre>

</td>

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

55

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

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

<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "ovStore.H"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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

<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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

<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

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

64

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="n" style="color: #333;">ovStore</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ovStore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">gkStore</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gkp</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); 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="530" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -525,12 +530,42 @@ ovStore::numOverlapsPerRead(uint32 numReads) {</td>

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525

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530

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

<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

526

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<td class="diff-line-num new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

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

<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

527

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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

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

<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">evalueFileMap</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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

<pre style="margin: 0;">+<span id="LC534" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

535

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

<pre style="margin: 0;">+<span id="LC535" class="line" lang="c">  <span class="n" style="color: #333;">evalueFileMap</span><span class="p">()</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="c">    <span class="n" style="color: #333;">_name</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

537

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="c">    <span class="n" style="color: #333;">_bgnID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="c">    <span class="n" style="color: #333;">_endID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

539

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

<pre style="margin: 0;">+<span id="LC539" class="line" lang="c">    <span class="n" style="color: #333;">_Nolap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

541

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

<pre style="margin: 0;">+<span id="LC541" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">char</span>     <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_name</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>    <span class="n" style="color: #333;">_bgnID</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="c">  <span class="n" style="color: #333;">uint32</span>    <span class="n" style="color: #333;">_endID</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="c">  <span class="n" style="color: #333;">uint64</span>    <span class="n" style="color: #333;">_Nolap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="c"><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

548

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

<pre style="margin: 0;">+<span id="LC548" class="line" lang="c"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

549

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="c"><span class="n" style="color: #333;">bool</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

550

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="c"><span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="n" style="color: #333;">evalueFileMap</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">evalueFileMap</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">_bgnID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">_bgnID</span><span class="p">);</span></span>

</pre>

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552

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="c"><span class="p">};</span></span>

</pre>

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553

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="c"></span>

</pre>

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554

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

555

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

528

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<td class="diff-line-num new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"><span class="n" style="color: #333;">ovStore</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addEvalues</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fileList</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

530

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<td class="diff-line-num new_line old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC530" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">char</span>  <span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">FILENAME_MAX</span></span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

531

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<td class="diff-line-num new_line old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC531" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">snprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FILENAME_MAX</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"%s/evalues"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_storePath</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">char</span>  <span class="n" style="color: #333;"><span class="idiff left">evalueName</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">FILENAME_MAX</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

559

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff">  </span><span class="n" style="color: #333;"><span class="idiff">evalueTemp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">FILENAME_MAX</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

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<td class="diff-line-num new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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

<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"></span>

</pre>

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533

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<td class="diff-line-num new_line old" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC533" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If we have an opened memory mapped file, close it.</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Handy to have the name of the file we're working with.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

562

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="c">  <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">evalueTemp</span><span class="p">,</span> <span class="n" style="color: #333;">FILENAME_MAX</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s/evalues.WORKING"</span><span class="p">,</span> <span class="n" style="color: #333;">_storePath</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="c">  <span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">evalueName</span><span class="p">,</span> <span class="n" style="color: #333;">FILENAME_MAX</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s/evalues"</span><span class="p">,</span>         <span class="n" style="color: #333;">_storePath</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

565

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

<pre style="margin: 0;">+<span id="LC565" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  If we have an opened memory mapped file, close it.  There _shouldn't_ be one,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

567

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  as it would exist only if evalues were already added, but it might.  And if it</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

568

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  does exist, nuke it from disk too (well, not quite yet).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

534

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<td class="diff-line-num new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

569

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

<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

535

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<td class="diff-line-num new_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

570

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_evaluesMap</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<td class="diff-line-num new_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="c">    <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">_evaluesMap</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); 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="574" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -539,76 +574,78 @@ ovStore::addEvalues(vector<char *> &fileList) {</td>

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<td class="diff-line-num old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<td class="diff-line-num new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

574

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

<pre style="margin: 0;"> <span id="LC574" class="line" lang="c">    <span class="n" style="color: #333;">_evalues</span>    <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<td class="diff-line-num new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

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

<pre style="margin: 0;"> <span id="LC575" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

</td>

<td class="diff-line-num new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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

<pre style="margin: 0;"> <span id="LC576" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

542

</td>

<td class="diff-line-num new_line old" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC542" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Allocate space for the evalues.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AS_UTL_fileExists</span><span class="p">(</span><span class="n" style="color: #333;">evalueName</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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

<pre style="margin: 0;">+<span id="LC578" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"WARNING:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"WARNING: existing evalue file will be overwritten!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

</td>

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

<pre style="margin: 0;">+<span id="LC580" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"WARNING:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

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

<pre style="margin: 0;">+<span id="LC581" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

</td>

<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

</td>

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

<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

544

</td>

<td class="diff-line-num new_line old" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC544" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">_evalues</span></span><span class="idiff">     </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">uint16</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">numOverlaps</span></span><span class="p"><span class="idiff right">()];</span></span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

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

<pre style="margin: 0;">+<span id="LC583" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  Scan each file, finding the first overlap in it.</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

</td>

<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

</td>

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

<pre style="margin: 0;"> <span id="LC584" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

546

</td>

<td class="diff-line-num new_line old" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC546" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Remove a bogus evalues file if one exists.</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

</td>

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

<pre style="margin: 0;">+<span id="LC585" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

</td>

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

<pre style="margin: 0;">+<span id="LC586" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Scanning.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

547

</td>

<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

</td>

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

<pre style="margin: 0;"> <span id="LC587" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

548

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC548" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">AS_UTL_fileExists</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

549

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC549" class="line" lang="c">      <span class="p">(</span><span class="n" style="color: #333;">AS_UTL_sizeOfFile</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_info</span><span class="p">.</span><span class="n" style="color: #333;">numOverlaps</span><span class="p">())))</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

550

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC550" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"WARNING: existing evalues file is incorrect size: should be "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" bytes, is "</span> <span class="n" style="color: #333;">F_U64</span> <span class="s" style="color: #d14;">" bytes.  Removing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

551

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC551" class="line" lang="c">            <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_info</span><span class="p">.</span><span class="n" style="color: #333;">numOverlaps</span><span class="p">()),</span> <span class="n" style="color: #333;">AS_UTL_sizeOfFile</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">));</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

552

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC552" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_unlink</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

553

</td>

<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC553" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

</td>

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

<pre style="margin: 0;">+<span id="LC588" class="line" lang="c">  <span class="n" style="color: #333;">evalueFileMap</span>   <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">emap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">evalueFileMap</span> <span class="p">[</span><span class="n" style="color: #333;">fileList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()];</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

554

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<td class="diff-line-num new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

589

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<pre style="margin: 0;"> <span id="LC589" class="line" lang="c"></span>

</pre>

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555

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<td class="diff-line-num new_line old" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC555" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Clear the evalues.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC590" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fileList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="c">    <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_name</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileList</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="c">    <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_bgnID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="c">    <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_endID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="c">    <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_Nolap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<td class="diff-line-num new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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

<pre style="margin: 0;"> <span id="LC595" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

557

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<td class="diff-line-num new_line old" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC557" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint64</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">_info</span><span class="p">.</span><span class="n" style="color: #333;">numOverlaps</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

558

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<td class="diff-line-num new_line old" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC558" class="line" lang="c">    <span class="n" style="color: #333;">_evalues</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT16_MAX</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">E</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AS_UTL_openInputFile</span><span class="p">(</span><span class="n" style="color: #333;">fileList</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<td class="diff-line-num new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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

<pre style="margin: 0;"> <span id="LC597" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

560

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC560" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  For each file in the fileList, open it, read the header (bgnID, endID and</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

561

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC561" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  number of values), load the evalues, then copy this data to the actual</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

562

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC562" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  evalues file.</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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

<pre style="margin: 0;">+<span id="LC598" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">AS_UTL_safeRead</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">E</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">_bgnID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"bgnID"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">uint32</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">AS_UTL_safeRead</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">E</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">_endID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"endID"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">uint32</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

600

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">AS_UTL_safeRead</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">E</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">_Nolap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Nolap"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">uint64</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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

<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

564

</td>

<td class="diff-line-num new_line old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC564" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fileList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

565

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<td class="diff-line-num new_line old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC565" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">bgnID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

566

</td>

<td class="diff-line-num new_line old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC566" class="line" lang="c">    <span class="n" style="color: #333;">uint32</span>        <span class="n" style="color: #333;">endID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

567

</td>

<td class="diff-line-num new_line old" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC567" class="line" lang="c">    <span class="n" style="color: #333;">uint64</span>        <span class="n" style="color: #333;">len</span>   <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

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

<pre style="margin: 0;">+<span id="LC602" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_closeFile</span><span class="p">(</span><span class="n" style="color: #333;">E</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

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<td class="diff-line-num new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

</td>

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

<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

569

</td>

<td class="diff-line-num new_line old" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC569" class="line" lang="c">    <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

570

</td>

<td class="diff-line-num new_line old" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC570" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">FILE</span>  <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">fileList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

571

</td>

<td class="diff-line-num new_line old" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC571" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

572

</td>

<td class="diff-line-num new_line old" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC572" class="line" lang="c">      <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to open evalues file '%s': %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;">fileList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)),</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

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

<pre style="margin: 0;">+<span id="LC604" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  '%s' covers reads %7"</span> <span class="n" style="color: #333;">F_U32P</span> <span class="s" style="color: #d14;">"-%-7"</span> <span class="n" style="color: #333;">F_U32P</span> <span class="s" style="color: #d14;">" with %10"</span> <span class="n" style="color: #333;">F_U64P</span> <span class="s" style="color: #d14;">" overlaps.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<pre style="margin: 0;">+<span id="LC605" class="line" lang="c">            <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_name</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_bgnID</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_endID</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_Nolap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

573

</td>

<td class="diff-line-num new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

607

</td>

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

<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

574

</td>

<td class="diff-line-num new_line old" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC574" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_safeRead</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bgnID</span><span class="p">,</span> <span class="s" style="color: #d14;">"loid"</span><span class="p">,</span>   <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

575

</td>

<td class="diff-line-num new_line old" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC575" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_safeRead</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endID</span><span class="p">,</span> <span class="s" style="color: #d14;">"hiid"</span><span class="p">,</span>   <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint32</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

576

</td>

<td class="diff-line-num new_line old" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC576" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_safeRead</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">len</span><span class="p">,</span>   <span class="s" style="color: #d14;">"len"</span><span class="p">,</span>    <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint64</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

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

<pre style="margin: 0;">+<span id="LC608" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Sort the emap by starting read.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

</td>

<td class="diff-line-num new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

</td>

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

<pre style="margin: 0;"> <span id="LC609" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

578

</td>

<td class="diff-line-num new_line old" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC578" class="line" lang="c">  <span class="idiff left">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//  Figure out the overlap ID for the first overlap associated with bgnID</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

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

<pre style="margin: 0;">+<span id="LC610" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">sort</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fileList</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">());</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

579

</td>

<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

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

<pre style="margin: 0;"> <span id="LC611" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

580

</td>

<td class="diff-line-num new_line old" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC580" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">setRange</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bgnID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">endID</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

</td>

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

<pre style="margin: 0;">+<span id="LC612" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  Check that all IDs are present.</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

</td>

<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

</td>

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

<pre style="margin: 0;"> <span id="LC613" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

582

</td>

<td class="diff-line-num new_line old" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC582" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//  Load data directly into the evalue array</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

</td>

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

<pre style="margin: 0;">+<span id="LC614" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</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;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fileList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

615

</td>

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

<pre style="margin: 0;">+<span id="LC615" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">_endID</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_bgnID</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

616

</td>

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

<pre style="margin: 0;">+<span id="LC616" class="line" lang="c">      <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Discontinuity between files '%s' and '%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;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</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;">_name</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_name</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

617

</td>

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

<pre style="margin: 0;">+<span id="LC617" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

</td>

<td class="diff-line-num new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

618

</td>

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

<pre style="margin: 0;"> <span id="LC618" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

584

</td>

<td class="diff-line-num new_line old" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC584" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-  Loading evalues from '%s' -- ID range "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U32</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-"</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U32</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" with "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U64</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" overlaps</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

585

</td>

<td class="diff-line-num new_line old" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC585" class="line" lang="c">  <span class="idiff left">          </span><span class="n" style="color: #333;"><span class="idiff">fileList</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bgnID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">endID</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">len</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

</td>

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

<pre style="margin: 0;">+<span id="LC619" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  Now just copy the new evalues to the real evalues file.  The inputs two 32-bit words and</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

620

</td>

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

<pre style="margin: 0;">+<span id="LC620" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//  a 64-bit word at the start we need to ignore.  That's 8 16-bit words.</span></span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

</td>

<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

</td>

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

<pre style="margin: 0;"> <span id="LC621" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

587

</td>

<td class="diff-line-num new_line old" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC587" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_safeRead</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">_evalues</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_offt</span><span class="p">.</span><span class="n" style="color: #333;">_overlapID</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalues"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint16</span><span class="p">),</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

</td>

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

<pre style="margin: 0;">+<span id="LC622" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

623

</td>

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

<pre style="margin: 0;">+<span id="LC623" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Merging.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

</td>

<td class="diff-line-num new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

</td>

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

<pre style="margin: 0;"> <span id="LC624" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

589

</td>

<td class="diff-line-num new_line old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC589" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_closeFile</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">fileList</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

590

</td>

<td class="diff-line-num new_line old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC590" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

</td>

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

<pre style="margin: 0;">+<span id="LC625" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">EO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AS_UTL_openOutputFile</span><span class="p">(</span><span class="n" style="color: #333;">evalueTemp</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

591

</td>

<td class="diff-line-num new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

</td>

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

<pre style="margin: 0;"> <span id="LC626" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

592

</td>

<td class="diff-line-num new_line old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC592" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Write the evalues to disk.</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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

<pre style="margin: 0;">+<span id="LC627" class="line" lang="c">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint32</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fileList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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

<pre style="margin: 0;">+<span id="LC628" class="line" lang="c">    <span class="n" style="color: #333;">uint16</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">uint16</span> <span class="p">[</span><span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_Nolap</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

</td>

<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

</td>

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

<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

594

</td>

<td class="diff-line-num new_line old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC594" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">fprintf</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Saving evalues file for "</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">F_U64</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" overlaps.</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">numOverlaps</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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

<pre style="margin: 0;">+<span id="LC630" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">AS_UTL_loadFile</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ev</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">emap</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">ii</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">_Nolap</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">8</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

</td>

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

<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

596

</td>

<td class="diff-line-num new_line old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC596" class="line" lang="c">  <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

597

</td>

<td class="diff-line-num new_line old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC597" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">F</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

598

</td>

<td class="diff-line-num new_line old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC598" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

599

</td>

<td class="diff-line-num new_line old" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC599" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failed to make evalues file '%s': %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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)),</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

</td>

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

<pre style="margin: 0;">+<span id="LC632" class="line" lang="c">    <span class="n" style="color: #333;">AS_UTL_safeWrite</span><span class="p">(</span><span class="n" style="color: #333;">EO</span><span class="p">,</span> <span class="n" style="color: #333;">ev</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalues"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">uint16</span><span class="p">),</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_Nolap</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

</td>

<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

</td>

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

<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

601

</td>

<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC601" class="line" lang="c">  <span class="n" style="color: #333;"><span class="idiff left">AS_UTL_safeWrite</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">F</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_evalues</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"evalues"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">uint16</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">numOverlaps</span></span><span class="p"><span class="idiff right">())</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

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

<pre style="margin: 0;">+<span id="LC634" class="line" lang="c">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">delete</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ev</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

</td>

<td class="diff-line-num new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

</td>

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

<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

603

</td>

<td class="diff-line-num new_line old" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC603" class="line" lang="c">  <span class="n" style="color: #333;">AS_UTL_closeFile</span><span class="p">(</span><span class="n" style="color: #333;">F</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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

<pre style="margin: 0;">+<span id="LC636" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"  '%s' covers reads %7"</span> <span class="n" style="color: #333;">F_U32P</span> <span class="s" style="color: #d14;">"-%-7"</span> <span class="n" style="color: #333;">F_U32P</span> <span class="s" style="color: #d14;">"; %10"</span> <span class="n" style="color: #333;">F_U64P</span> <span class="s" style="color: #d14;">" with overlaps.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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

<pre style="margin: 0;">+<span id="LC637" class="line" lang="c">            <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_name</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_bgnID</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_endID</span><span class="p">,</span> <span class="n" style="color: #333;">emap</span><span class="p">[</span><span class="n" style="color: #333;">ii</span><span class="p">].</span><span class="n" style="color: #333;">_Nolap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

638

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

<pre style="margin: 0;">+<span id="LC638" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

604

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<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

</td>

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

<pre style="margin: 0;"> <span id="LC639" class="line" lang="c"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

605

</td>

<td class="diff-line-num new_line old" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC605" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Clean up, and reopen the file.  Usually, we just delete the store after</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

606

</td>

<td class="diff-line-num new_line old" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC606" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  values are loaded, so this is pointless.</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

640

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

<pre style="margin: 0;">+<span id="LC640" class="line" lang="c">  <span class="n" style="color: #333;">AS_UTL_closeFile</span><span class="p">(</span><span class="n" style="color: #333;">EO</span><span class="p">,</span> <span class="n" style="color: #333;">evalueTemp</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

607

</td>

<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

</td>

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

<pre style="margin: 0;"> <span id="LC641" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

608

</td>

<td class="diff-line-num new_line old" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC608" class="line" lang="c">  <span class="n" style="color: #333;">delete</span> <span class="p">[]</span> <span class="n" style="color: #333;">_evalues</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

642

</td>

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

<pre style="margin: 0;">+<span id="LC642" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

</td>

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

<pre style="margin: 0;">+<span id="LC643" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Renaming.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

</td>

<td class="diff-line-num new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

644

</td>

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

<pre style="margin: 0;"> <span id="LC644" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

610

</td>

<td class="diff-line-num new_line old" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC610" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//  Open the evalues file if it isn't already opened</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

</td>

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

<pre style="margin: 0;">+<span id="LC645" class="line" lang="c">  <span class="n" style="color: #333;">AS_UTL_unlink</span><span class="p">(</span><span class="n" style="color: #333;">evalueName</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

</td>

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

<pre style="margin: 0;">+<span id="LC646" class="line" lang="c">  <span class="n" style="color: #333;">AS_UTL_rename</span><span class="p">(</span><span class="n" style="color: #333;">evalueTemp</span><span class="p">,</span> <span class="n" style="color: #333;">evalueName</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

</td>

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

<pre style="margin: 0;"> <span id="LC647" class="line" lang="c"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

612

</td>

<td class="diff-line-num new_line old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC612" class="line" lang="c">  <span class="n" style="color: #333;">_evaluesMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">memoryMappedFile</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">memoryMappedFile_readOnly</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

613

</td>

<td class="diff-line-num new_line old" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC613" class="line" lang="c">  <span class="n" style="color: #333;">_evalues</span>    <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">uint16</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">_evaluesMap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

648

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

<pre style="margin: 0;">+<span id="LC648" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

649

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

<pre style="margin: 0;">+<span id="LC649" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Success!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

650

</td>

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

<pre style="margin: 0;">+<span id="LC650" class="line" lang="c">  <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

614

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

</td>

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

<pre style="margin: 0;"> <span id="LC651" class="line" lang="c"><span class="p">}</span></span></pre>

</td>

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