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GitLab

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<h3>

Andreas Tille pushed to branch debian/jessie-backports

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/84391d0e9496f60a31ee182bbf44dc1d7075bd3c">84391d0e</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2016-10-16T15:14:19-07:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump minimum required libguava-java version

We otherwise get the compilation error:

[ERROR] /<<BUILDDIR>>/mhap-2.1+dfsg/src/main/java/edu/umd/marbl/mhap/sketch/FrequencyCounts.java:[104,27] error:

no suitable method found for create((value,sin[...]alue),long,double)

The MHAP pom file specifies v19 and we still get this build error with v18,

so it seems to be a necessary minimum version.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/7cb51cbd3509bc4e9106b256b3274310a08c054f">7cb51cbd</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2016-10-16T15:15:28-07:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare new revision

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/c8088c376039cf94c347f7362358532e82c5fad5">c8088c37</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2017-07-21T13:33:05+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Added ref to OMICtools

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/3110815fd52d4eeb6ca193a25d0b567d42478f54">3110815f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2017-08-17T19:16:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix yaml syntax

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/1cb04d5d12dc48d904ab8609be7fd1c97acace26">1cb04d5d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2017-10-20T10:09:25+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix OMICS entry

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/7520c50250e80c570989db806d52702487baaab5">7520c502</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2018-03-15T23:59:53-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.3+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/24b6700418838698d5cd8d0d2a9093b682a20222">24b67004</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2018-03-15T23:59:54-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/2.1.3+dfsg'

Upstream version 2.1.3+dfsg

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/88230ca92f22c59e44af826fa8959bbe0936524c">88230ca9</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2018-03-16T00:01:17-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version 4.1.3

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/eaf20dbf36384bc7b4bbad657a134fef98e1e0de">eaf20dbf</a></strong>

<div>

<span>by Afif Elghraoui</span>

<i>at 2018-03-16T00:07:21-04:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">releasing package mhap version 2.1.3+dfsg-1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/32d6d67843170e1edd404b608203042279a35e0b">32d6d678</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:11:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into debian/jessie-backports

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/3ebd2ce78fbe3768cf807d02b2a95b592a2f057e">3ebd2ce7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:12:24+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">This is an inofficial backport since jessie-backports-sloppy will not supported any more

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mhap/commit/ef042b49e04879970d8537a1ef7c967f59f3f67f">ef042b49</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-07-17T12:40:26+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unnecessary ending newline patch which does not apply in Jessie

</pre>

</li>

</ul>

<h4>22 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#b98fa7af01889416914396da63ca9d77dfe4252b">

debian/patches/maven-artifacts.patch

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

debian/upstream/metadata

</a>

</li>

<li class="file-stats">

<a href="#2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c">

docs/source/installation.rst

</a>

</li>

<li class="file-stats">

<a href="#442292b8a7efeabbe4cc176709b833b1792140ec">

pom.xml

</a>

</li>

<li class="file-stats">

<a href="#b192944bcf196dd6baef80661669d3180c2c2a76">

src/main/java/edu/umd/marbl/mhap/impl/AbstractMatchSearch.java

</a>

</li>

<li class="file-stats">

<a href="#0c8d65f743b70c6649782d6b224d9e82e458d04c">

src/main/java/edu/umd/marbl/mhap/impl/FastaData.java

</a>

</li>

<li class="file-stats">

<a href="#377320ef841a8477eb72e607f13fe29db120a9d6">

src/main/java/edu/umd/marbl/mhap/impl/MinHashBitSequenceSubSketches.java

</a>

</li>

<li class="file-stats">

<a href="#0f487860355375928e02739ea9ae9b58c9c51caf">

src/main/java/edu/umd/marbl/mhap/impl/MinHashSearch.java

</a>

</li>

<li class="file-stats">

<a href="#108ea35d874acd6f7c4b34771c7f5098ec9f5ea6">

src/main/java/edu/umd/marbl/mhap/impl/SequenceSketch.java

</a>

</li>

<li class="file-stats">

<a href="#4648a85d8210c9489102662ae792a7c51cfe6874">

src/main/java/edu/umd/marbl/mhap/impl/SequenceSketchStreamer.java

</a>

</li>

<li class="file-stats">

<a href="#786de2062f4d0c39a1835c8026f96d8ecbe3cb13">

src/main/java/edu/umd/marbl/mhap/main/KmerStatSimulator.java

</a>

</li>

<li class="file-stats">

<a href="#ba4344791876a3da5cd1dd7dfc3b47194d383fdc">

src/main/java/edu/umd/marbl/mhap/main/MhapMain.java

</a>

</li>

<li class="file-stats">

<a href="#148367d1edb07892fef68aa2439e944ddf44cd67">

src/main/java/edu/umd/marbl/mhap/sketch/BottomOverlapSketch.java

</a>

</li>

<li class="file-stats">

<a href="#1e41d87bd924d9b454d2e6a063050b66a4c558f7">

src/main/java/edu/umd/marbl/mhap/sketch/BottomSketch.java

</a>

</li>

<li class="file-stats">

<a href="#69fffa1e5dcd79efea80f6ce8db10a383eaf79c6">

src/main/java/edu/umd/marbl/mhap/sketch/FrequencyCounts.java

</a>

</li>

<li class="file-stats">

<a href="#ff6aa275e4b4c1fa06704090afb1c5cafaaea820">

src/main/java/edu/umd/marbl/mhap/sketch/HashUtils.java

</a>

</li>

<li class="file-stats">

<a href="#bc59179d9c4f81f60f7286c877f4f65d3072327b">

src/main/java/edu/umd/marbl/mhap/sketch/MinHashBitSketch.java

</a>

</li>

<li class="file-stats">

<a href="#56e3977de1abb5faadbbd6204900ae0f13504014">

src/main/java/edu/umd/marbl/mhap/sketch/MinHashSketch.java

</a>

</li>

<li class="file-stats">

<a href="#1a74da5211d7ca610f86db293745349b5150cf22">

src/main/java/edu/umd/marbl/mhap/utils/Utils.java

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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 match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,12 +8,12 @@ You must have a recent  [JDK](http://www.oracle.com/technetwork/java/javase/down</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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

</td>

<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

</td>

<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="markdown"><span class="sb" style="color: #d14;">    git clone https://github.com/marbl/MHAP.git</span></span>

</pre>

</td>

</tr>

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

<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

</td>

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

10

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #d14;">    cd MHAP</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="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

</td>

<td class="diff-line-num new_line old" 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">

</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="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;">    m<span class="idiff left right">ave</span>n install</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="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">

</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="markdown"><span class="sb" style="color: #d14;">    m<span class="idiff left right">v</span>n install</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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="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="markdown"><span class="sb" style="color: #d14;">    </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="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="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">

</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="markdown">For a quick user-quide, run:</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="markdown"><span class="idiff left right">Maven executables vary by system, it could also be maven/mvn/mv32, depending on your installation. </span>For a quick user-quide, run:</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="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>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>

</pre>

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15

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

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;">    cd target</span></span>

</pre>

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

16

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<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">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;">    java -jar mhap-2.1.<span class="idiff left right">1</span>.jar</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); 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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;">    java -jar mhap-2.1.<span class="idiff left right">3</span>.jar</span></span>

</pre>

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<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

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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">

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

</pre>

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<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="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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Docs</span></span>

</pre>

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<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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">For the full documentation information please see http://mhap.readthedocs.io/en/latest/</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#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">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mhap (2.1.3+dfsg-1~bpo8+1) jessie-backports; urgency=medium</span>

</pre>

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<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">

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<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

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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="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

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<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">

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<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

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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="LC3" class="line" lang="plaintext">  * Rebuild for jessie-backports.</span>

</pre>

</td>

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<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">

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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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<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"></span>

</pre>

</td>

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<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">

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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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 17 Jul 2018 12:11:51 +0200</span>

</pre>

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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"></span>

</pre>

</td>

</tr>

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<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">

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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">mhap (2.1.3+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

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<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">

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<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"></span>

</pre>

</td>

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<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">

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<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

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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="LC9" class="line" lang="plaintext">  [ Afif Elghraoui ]</span>

</pre>

</td>

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<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">

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<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

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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="LC10" class="line" lang="plaintext">  * Bump minimum required libguava-java version</span>

</pre>

</td>

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<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">

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

11

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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="LC11" class="line" lang="plaintext">  * New upstream version 2.1.3+dfsg</span>

</pre>

</td>

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<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">

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<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

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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="LC12" class="line" lang="plaintext">  * Standards-Version 4.1.3</span>

</pre>

</td>

</tr>

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<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">

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

13

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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="LC13" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<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">

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<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">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">  [ Steffen Moeller, Andreas Tille ]</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">  * Added ref to OMICtools</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Afif Elghraoui <afif@debian.org>  Fri, 16 Mar 2018 00:05:16 -0400</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">mhap (2.1.1+dfsg-1~bpo8+1) jessie-backports; urgency=medium</span>

</pre>

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

</pre>

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3

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">  * Rebuild for jessie-backports.</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ Build-Depends:</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">     libguava-java (>= 19),</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">     libssw-java,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.8</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.1.3</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://mhap.readthedocs.org/en/stable/</span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/mhap.git</span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mhap.git</span>

</pre>

</td>

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<br>

</li>

<li id="b98fa7af01889416914396da63ca9d77dfe4252b">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#b98fa7af01889416914396da63ca9d77dfe4252b"><strong>debian/patches/maven-artifacts.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,8 +2,8 @@ Description: Tell maven how to find libraries without maven artifacts</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> This change was made with help from Tony Mancill <tmancill@debian.org></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Forwarded: not-needed</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">mhap.orig</span>/pom.xml</span></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">mhap</span>/pom.xml</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/pom.xml</span></span>

</pre>

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<td class="diff-line-num new old_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">

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/pom.xml</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -110,6 +110,8 @@</span></span>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">                   <groupId>it.unimi.dsi</groupId></span>

</pre>

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

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<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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff">                   <artifactId>fastutil</artifactId></span>

</pre>

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

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,10 +13,3 @@ Forwarded: not-needed</td>

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13

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13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff">          </dependency></span>

</pre>

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

14

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff">          <dependency></span>

</pre>

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

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15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff">                  <groupId>org.apache.commons</groupId></span></pre>

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<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">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,4 +136,4 @@</span></span>

</pre>

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<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">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">  </dependencies></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<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">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">  <url>https://github.com/marbl/MHAP</url></span>

</pre>

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

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<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">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">  <description>MinHash alignment process (MHAP pronounced MAP): locality sensitive hashing to detect overlaps and utilities.</description></span>

</pre>

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<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">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</project></span></span>

</pre>

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

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<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">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">\ No newline at end of file</span>

</pre>

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

22

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<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">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</project></span></span></pre>

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<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,3 +9,6 @@ Reference:</td>

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<td class="diff-line-num old_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="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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  DOI: 10.1038/nbt.3238</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="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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  PMID: 26006009</span>

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  URL: http://www.nature.com/nbt/journal/v33/n6/full/nbt.3238.html</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  - Name: OMICtools</span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">    Entry: OMICS_13515</span></pre>

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<br>

</li>

<li id="2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#2d9c0c62cdf7d42edd7e9a56b0879a0286f40f1c"><strong>docs/source/installation.rst</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -28,19 +28,25 @@ The pre-compiled version is recommended to users who want to run MHAP, without d</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">.. code-block:: bash</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">    $ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.<span class="idiff left right">t</span>ar.gz</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">    $ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.<span class="idiff left right">j</span>ar.gz</span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">And if ``wget`` not available, you can use ``curl`` instead:</span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">    $ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.<span class="idiff left right">tar.gz > mhap-2.1.1.t</span>ar.gz</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); 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="37" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC37" class="line" lang="plaintext">    $ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.<span class="idiff left right">j</span>ar.gz</span>

</pre>

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

<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="plaintext">Then run</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(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="40" style="width: 35px; color: rgba(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="LC40" class="line" lang="plaintext"></span>

</pre>

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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">

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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">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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42

</td>

<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

</td>

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

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></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="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

43

</td>

<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC43" class="line" lang="plaintext">   $ tar xvzf mhap-2.1.1.tar.gz</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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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="LC43" class="line" lang="plaintext">   $ gunzip mhap-2.1.1.jar.gz</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="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">

</td>

<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">

44

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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="LC44" 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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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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="LC45" class="line" lang="plaintext">Now to run mhap</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_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">

46

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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="LC46" class="line" lang="plaintext"></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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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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="LC47" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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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="LC48" 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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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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="LC49" class="line" lang="plaintext">   $ java -jar mhap-2.1.1.jar</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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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="LC50" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

</td>

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

<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Source</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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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="LC52" class="line" lang="plaintext">-----------------</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="442292b8a7efeabbe4cc176709b833b1792140ec">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#442292b8a7efeabbe4cc176709b833b1792140ec"><strong>pom.xml</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 match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold 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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>

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<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

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

3

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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="LC3" class="line" lang="xml">    <span class="nt" style="color: navy;"><modelVersion></span>4.0.0<span class="nt" style="color: navy;"></modelVersion></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="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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml">    <span class="nt" style="color: navy;"><groupId></span>mhap<span class="nt" style="color: navy;"></groupId></span></span>

</pre>

</td>

</tr>

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

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

5

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

5

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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="LC5" class="line" lang="xml">    <span class="nt" style="color: navy;"><artifactId></span>mhap<span class="nt" style="color: navy;"></artifactId></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC6" class="line" lang="xml">    <span class="nt" style="color: navy;"><version></span>2.1.<span class="idiff left right">1</span><span class="nt" style="color: navy;"></version></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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="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="xml">    <span class="nt" style="color: navy;"><version></span>2.1.<span class="idiff left right">3</span><span class="nt" style="color: navy;"></version></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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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="LC7" class="line" lang="xml">    <span class="nt" style="color: navy;"><name></span>MinHash Alignment Process<span class="nt" style="color: navy;"></name></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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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="LC8" class="line" lang="xml">    <span class="nt" style="color: navy;"><build></span></span>

</pre>

</td>

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<td class="diff-line-num old_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="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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="xml">            <span class="nt" style="color: navy;"><resources></span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="xml">  <span class="nt" style="color: navy;"></dependencies></span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="xml">  <span class="nt" style="color: navy;"><url></span>https://github.com/marbl/MHAP<span class="nt" style="color: navy;"></url></span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="xml">  <span class="nt" style="color: navy;"><description></span>MinHash alignment process (MHAP pronounced MAP): locality sensitive hashing to detect overlaps and utilities.<span class="nt" style="color: navy;"></description></span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="xml"><span class="nt" style="color: navy;"></project></span></span></pre>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="xml">  <span class="nt" style="color: navy;"><properties></span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="xml">          <span class="nt" style="color: navy;"><project.build.sourceEncoding></span>UTF-8<span class="nt" style="color: navy;"></project.build.sourceEncoding></span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="xml">  <span class="nt" style="color: navy;"></properties></span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="xml"><span class="nt" style="color: navy;"></project></span></span></pre>

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<br>

</li>

<li id="b192944bcf196dd6baef80661669d3180c2c2a76">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#b192944bcf196dd6baef80661669d3180c2c2a76"><strong>src/main/java/edu/umd/marbl/mhap/impl/AbstractMatchSearch.java</strong></a>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequencesSearched</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AtomicLong</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java">  <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addData</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SequenceSketchStreamer</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java">  <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addData</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SequenceSketchStreamer</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// figure out number of cores</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java">          <span class="n" style="color: #333;">ExecutorService</span> <span class="n" style="color: #333;">execSvc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Executors</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newFixedThreadPool</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numThreads</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +80,7 @@ public abstract class AbstractMatchSearch</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">                                  <span class="k" style="font-weight: 600;">try</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">                                  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">                                          <span class="n" style="color: #333;">ReadBuffer</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ReadBuffer</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num old old_line" 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="LC83" class="line" lang="java">                                          <span class="n" style="color: #333;">SequenceSketch</span> <span class="n" style="color: #333;">seqHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dequeue</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;"><span class="idiff left right">false</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_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="LC83" class="line" lang="java">                                          <span class="n" style="color: #333;">SequenceSketch</span> <span class="n" style="color: #333;">seqHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">dequeue</span><span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java">                                          <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seqHashes</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">                                          <span class="o" style="font-weight: 600;">{</span></span>

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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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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java">                                                  <span class="n" style="color: #333;">addSequence</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seqHashes</span><span class="o" style="font-weight: 600;">);</span></span>

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<br>

</li>

<li id="0c8d65f743b70c6649782d6b224d9e82e458d04c">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#0c8d65f743b70c6649782d6b224d9e82e458d04c"><strong>src/main/java/edu/umd/marbl/mhap/impl/FastaData.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +126,8 @@ public class FastaData implements Cloneable</td>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java">         <span class="n" style="color: #333;">StringBuilder</span> <span class="n" style="color: #333;">fastaSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC129" class="line" lang="java"></span>

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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">

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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">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">offset</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="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">

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

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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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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java">         <span class="kd" style="font-weight: 600;">synchronized</span> <span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fileReader</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readFullFile</span><span class="o" style="font-weight: 600;">)</span></span>

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

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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">@@ -175,13 +176,14 @@ public class FastaData implements Cloneable</td>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">                         <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fastaSeq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java">                         <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numberProcessed</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">incrementAndGet</span><span class="o" style="font-weight: 600;">();</span>                      </span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span>                      </span>

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

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">fastaSeqSring</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastaSeq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">fastaSeqSring</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isEmpty</span><span class="o" style="font-weight: 600;">())</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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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="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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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numberProcessed</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">incrementAndGet</span><span class="o" style="font-weight: 600;">();</span></span>

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

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">//generate sequence id</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="java">                 <span class="n" style="color: #333;">SequenceId</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceId</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">STORE_FULL_ID</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<li id="377320ef841a8477eb72e607f13fe29db120a9d6">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#377320ef841a8477eb72e607f13fe29db120a9d6"><strong>src/main/java/edu/umd/marbl/mhap/impl/MinHashBitSequenceSubSketches.java</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">@@ -61,7 +61,7 @@ public final class MinHashBitSequenceSubSketches</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">stepSize</span><span class="o" style="font-weight: 600;">);</span>                       </span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//compute minhashes</span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sketch</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currStart</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;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sketch</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currStart</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;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">                  </span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">                  <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashBitSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sketch</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">                  </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">@@ -91,7 +91,7 @@ public final class MinHashBitSequenceSubSketches</td>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">currStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">stepSize</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>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//compute minhashes</span></span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java">                  <span class="n" style="color: #333;">sketches</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashBitSketch</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currStart</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;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">                  <span class="n" style="color: #333;">sketches</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashBitSketch</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currStart</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;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">                  </span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java">                  <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">stepSize</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="0f487860355375928e02739ea9ae9b58c9c51caf">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#0f487860355375928e02739ea9ae9b58c9c51caf"><strong>src/main/java/edu/umd/marbl/mhap/impl/MinHashSearch.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +61,7 @@ public final class MinHashSearch extends AbstractMatchSearch</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SequenceId</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">SequenceSketch</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequenceVectorsHash</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">  </span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceSketchStreamer</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numMinMatches</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">,</span> </span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">storeResults</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minStoreLength</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxShift</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">acceptScore</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">storeResults</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minStoreLength</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxShift</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">acceptScore</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</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;">storeResults</span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,8 +91,8 @@ public final class MinHashSearch extends AbstractMatchSearch</td>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">                  <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">          </span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java">          <span class="n" style="color: #333;"><span class="idiff left">addData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">);</span></span></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java">          </span>

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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">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//store both forward andd reverse</span></span></span>

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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">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java">          <span class="n" style="color: #333;"><span class="idiff left">addData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></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">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">);</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java">          </span>

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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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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java">          <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Stored "</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequenceVectorsHash</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">" sequences in the index."</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<br>

</li>

<li id="108ea35d874acd6f7c4b34771c7f5098ec9f5ea6">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#108ea35d874acd6f7c4b34771c7f5098ec9f5ea6"><strong>src/main/java/edu/umd/marbl/mhap/impl/SequenceSketch.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<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">@@ -67,8 +67,10 @@ public final class SequenceSketch implements Serializable</td>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// dos.writeBoolean(this.id.isForward());</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isFwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readBoolean</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// dos.writeInt(this.id.getHeaderId());</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java">                  <span class="n" style="color: #333;">SequenceId</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SequenceId</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readLong</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isFwd</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="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="LC70" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// dos.writeLong(this.id.getHeaderId());</span></span>

</pre>

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<td class="diff-line-num new old_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="LC71" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">// dos.writeUTF(this.id.getHeader());</span></span>

</pre>

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<td class="diff-line-num new old_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="java">                  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java">                  <span class="n" style="color: #333;">SequenceId</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SequenceId</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readLong</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isFwd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readUTF</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java">                  </span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java">                  <span class="c1" style="color: #998; font-style: italic;">//dos.writeInt(this.sequenceLength);</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sequenceLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readInt</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -101,13 +103,16 @@ public final class SequenceSketch implements Serializable</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orderedHashes</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequenceLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getId</span><span class="o" style="font-weight: 600;">();</span></span>

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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="LC108" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">mainHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSquenceString</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java">         </span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomOverlapSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSquenceString</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">orderedSketchSize</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="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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<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="java">         <span class="c1" style="color: #998; font-style: italic;">//do not do reverse compliment for minhash, since unordered</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">mainHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSquenceString</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">repeatWeight</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="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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<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="java">         </span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//do not do reverse compliment</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomOverlapSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSquenceString</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceSketch</span> <span class="nf" style="color: #900; font-weight: 600;">createOffset</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +133,7 @@ public final class SequenceSketch implements Serializable</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writeBoolean</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">id</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isForward</span><span class="o" style="font-weight: 600;">());</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="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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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writeLong</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">id</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeaderId</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="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">

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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="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writeUTF</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">id</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeader</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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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="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writeInt</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sequenceLength</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mainHashesBytes</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java">                 <span class="n" style="color: #333;">dos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">orderedHashesBytes</span><span class="o" style="font-weight: 600;">);</span></span>

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<br>

</li>

<li id="4648a85d8210c9489102662ae792a7c51cfe6874">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#4648a85d8210c9489102662ae792a7c51cfe6874"><strong>src/main/java/edu/umd/marbl/mhap/impl/SequenceSketchStreamer.java</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,6 +66,7 @@ public class SequenceSketchStreamer</td>

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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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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"></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">

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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">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedSketchSize</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">readClosed</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">readingFasta</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ConcurrentLinkedQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SequenceSketch</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sequenceHashList</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,6 +80,7 @@ public class SequenceSketchStreamer</td>

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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">

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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="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_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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<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="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">repeatWeight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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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">

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minOlapLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minOlapLength</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_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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<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="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">doReverseCompliment</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>

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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="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">

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"></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="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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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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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">

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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="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +93,7 @@ public class SequenceSketchStreamer</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceSketchStreamer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minOlapLength</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java">                  <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java">                  <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">fastaData</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastaData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readingFasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -99,7 +101,8 @@ public class SequenceSketchStreamer</td>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numberProcessed</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">AtomicLong</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">repeatWeight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minOlapLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minOlapLength</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<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="LC102" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">doReverseCompliment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java">         </span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -259,7 +262,7 @@ public class SequenceSketchStreamer</td>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceSketch</span> <span class="nf" style="color: #900; font-weight: 600;">getSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// compute the hashes</span></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">repeatWeight</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="na" style="color: teal;">repeatWeight</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processAddition</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceSketch</span> <span class="n" style="color: #333;">seqHashes</span><span class="o" style="font-weight: 600;">)</span></span>

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<br>

</li>

<li id="786de2062f4d0c39a1835c8026f96d8ecbe3cb13">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#786de2062f4d0c39a1835c8026f96d8ecbe3cb13"><strong>src/main/java/edu/umd/marbl/mhap/main/KmerStatSimulator.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,15 +187,15 @@ public class KmerStatSimulator {</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="java"> </span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">compareMinHash</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java">         <span class="n" style="color: #333;">BottomSketch</span> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</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="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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC191" class="line" lang="java">         <span class="n" style="color: #333;">BottomSketch</span> <span class="n" style="color: #333;">h2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</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="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java">         <span class="n" style="color: #333;">BottomSketch</span> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></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="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC191" class="line" lang="java">         <span class="n" style="color: #333;">BottomSketch</span> <span class="n" style="color: #333;">h2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">true</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(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="LC192" class="line" lang="java">         </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="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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<pre style="margin: 0;"> <span id="LC193" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">jaccard</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<td class="diff-line-num new_line" data-linenumber="194" style="width: 35px; color: rgba(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="LC194" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</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">

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">compareMinHash2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</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="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="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">

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java">         <span class="n" style="color: #333;">MinHashSketch</span> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</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="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

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<td class="diff-line-num new_line old" 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">

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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="LC198" class="line" lang="java">         <span class="n" style="color: #333;">MinHashSketch</span> <span class="n" style="color: #333;">h2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</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="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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

<pre style="margin: 0;">+<span id="LC197" class="line" lang="java">         <span class="n" style="color: #333;">MinHashSketch</span> <span class="n" style="color: #333;">h1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;"><span class="idiff left">true</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="mf" style="color: #099;">1.0</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="199" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

198

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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="LC198" class="line" lang="java">         <span class="n" style="color: #333;">MinHashSketch</span> <span class="n" style="color: #333;">h2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmer</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1256</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;"><span class="idiff left">true</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java">         </span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">h1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">jaccard</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h2</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="ba4344791876a3da5cd1dd7dfc3b47194d383fdc">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#ba4344791876a3da5cd1dd7dfc3b47194d383fdc"><strong>src/main/java/edu/umd/marbl/mhap/main/MhapMain.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,11 +62,14 @@ public final class MhapMain</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">processFile</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">toFile</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"></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="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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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">DEFAULT_OVERLAP_ACCEPT_SCORE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.78</span><span class="o" style="font-weight: 600;">;</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="java"></span>

</pre>

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<td class="diff-line-num 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">

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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="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">DEFAULT_REPEAT_WEIGHT</span><span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.9</span><span class="o" style="font-weight: 600;">;</span></span>

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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="java"></span>

</pre>

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<td class="diff-line-num new old_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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<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="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">DEFAULT_REPEAT_IDF_SCALE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">3.0</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="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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<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="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">DEFAULT_FILTER_CUTOFF</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">DEFAULT_KMER_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="o" style="font-weight: 600;">;</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">@@ -101,22 +104,24 @@ public final class MhapMain</td>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-q"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Usage 1: The FASTA file of reads, or a directory of files, that will be compared to the set of reads in the box (see -s). Usage 2: The output directory for the binary formatted dat files."</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>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-p"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Usage 2 only. The directory containing FASTA files that should be converted to binary format for storage."</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>

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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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-f"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"k-mer filter file used for filtering out highly repetative k-mers. Must be sorted in descending order of frequency (second column)."</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>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-k"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], k-mer size used for MinHashing. The k-mer size for second stage filter is seperate, and can<span class="idiff left right">not</span> be modified."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_KMER_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-hashes"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], <span class="idiff left right">n</span>umber of min-mers to be used in MinHashing."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_WORDS</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--threshold"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">t</span>he threshold cutoff for the second stage sort-merge filter. This is based on the identity score computed from the Jaccard distance of k-mers (size given by ordered-kmer-size) in the overlapping regions."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_OVERLAP_ACCEPT_SCORE</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--filter-threshold"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">t</span>he cutoff at which the k-mer in the k-mer filter file is considered repetitive. This value for a specific k-mer is specified in the second column in the filter file. If no filter file is provided, this option is ignored."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_FILTER_CUTOFF</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--max-shift"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">r</span>egion size to the left and right of the estimated overlap, as derived from the median shift and sequence length, where a k-mer matches are still considered valid. Second stage filter only."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_MAX_SHIFT_PERCENT</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-min-matches"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], <span class="idiff left right">m</span>inimum # min-mer that must be shared before computing second stage filter. Any sequences below that value are considered non-overlapping."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_MIN_MATCHES</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-threads"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], number of threads to use for computation. Typically set to #cores."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_THREADS</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_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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<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-k"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], k-mer size used for MinHashing. The k-mer size for second stage filter is seperate, and can<span class="idiff left right"> also</span> be modified."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_KMER_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-hashes"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], <span class="idiff left right">N</span>umber of min-mers to be used in MinHashing."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_WORDS</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_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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<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--threshold"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">T</span>he threshold cutoff for the second stage sort-merge filter. This is based on the identity score computed from the Jaccard distance of k-mers (size given by ordered-kmer-size) in the overlapping regions."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_OVERLAP_ACCEPT_SCORE</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="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">

</td>

<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--filter-threshold"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">T</span>he cutoff at which the k-mer in the k-mer filter file is considered repetitive. This value for a specific k-mer is specified in the second column in the filter file. If no filter file is provided, this option is ignored."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_FILTER_CUTOFF</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="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">

</td>

<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--max-shift"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double], <span class="idiff left right">R</span>egion size to the left and right of the estimated overlap, as derived from the median shift and sequence length, where a k-mer matches are still considered valid. Second stage filter only."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_MAX_SHIFT_PERCENT</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="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">

</td>

<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-min-matches"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], <span class="idiff left right">M</span>inimum # min-mer that must be shared before computing second stage filter. Any sequences below that value are considered non-overlapping."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_MIN_MATCHES</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="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">

</td>

<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--num-threads"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], n<span class="idiff left right">N</span>umber of threads to use for computation. Typically set to #cores."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_NUM_THREADS</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(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="LC114" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--repeat-weight"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double] Repeat suppression strength for tf-idf weighing. <0.0 do unweighted MinHash (version 1.0), >=1.0 do only the tf weighing. To perform no idf weighting, do no supply -f option. "</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_REPEAT_WEIGHT</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="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="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--repeat-idf-scale"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[double] The upper range of the idf (from tf-idf) scale. The full scale will be [1,X], where X is the parameter."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_REPEAT_IDF_SCALE</span><span class="o" style="font-weight: 600;">);</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">

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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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--ordered-kmer-size"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int] The size of k-mers used in the ordered second stage filter."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_ORDERED_KMER_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--ordered-sketch-size"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int] The sketch size for second stage filter."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_ORDERED_SKETCH_SIZE</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(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="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--min-store-length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], The minimum length of the read that is stored in the box. Used to filter out short reads from FASTA file."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_MIN_STORE_LENGTH</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_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">

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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">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--min-olap-length"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int], The minimum length of the read that used for overlapping. Used to filter out short reads from FASTA file."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_MIN_OVL_LENGTH</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_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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<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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--no-self"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Do not compute the overlaps between sequences inside a box. Should be used when the to and from sequences are coming from different files."</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</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="117" style="width: 35px; color: rgba(0,0,0,0.3); 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="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--store-full-id"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Store full IDs as seen in FASTA file<span class="idiff left right">, rather than storing just the sequence position in the file. Some FASTA files have long IDS, slowing output of results. This options is ignored when using compressed file format</span>."</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</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="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">

</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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--store-full-id"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Store full IDs as seen in FASTA file<span class="idiff left right">s, rather than storing just the sequence position in the file. Some FASTA files have long IDS, slowing output of results. This options is ignored when using compressed file format. Indexed file (-s) is indexed first, followed by -q files in alphabetical order</span>."</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="diff-line-num new_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">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--supress-noise"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"[int] 0) Does nothing, 1) completely removes any k-mers not specified in the filter file, 2) supresses k-mers not specified in the filter file, similar to repeats. "</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--no-tf"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Do not perform the tf weighing, in the tf-idf weighing."</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</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="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">

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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="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--no-rc"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Do not store or do comparison of the reverse compliment strings."</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">);</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="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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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java">         <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addOption</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--settings"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Set all unset parameters for the default settings. Same defaults are applied to Nanopore and Pacbio reads. 0) None, 1) Default, 2) Fast, 3) Sensitive."</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</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="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="java">         </span>

</pre>

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<td class="diff-line-num 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">

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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="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -264,6 +269,13 @@ public final class MhapMain</td>

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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="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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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="270" style="width: 35px; color: rgba(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="LC270" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_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="LC271" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//check range</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--repeat-idf-scale"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getDouble</span><span class="o" style="font-weight: 600;">()<</span><span class="mf" style="color: #099;">1.0</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="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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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

273

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"The minimum repeat idf scale must be >=1.0."</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="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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<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="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exit</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>

</pre>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java"></span>

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<td class="diff-line-num new old_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="LC278" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//check range</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--max-shift"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getDouble</span><span class="o" style="font-weight: 600;">()<-</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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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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<pre style="margin: 0;"> <span id="LC281" class="line" lang="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"The minimum shift must be greater than -1."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -322,6 +334,7 @@ public final class MhapMain</td>

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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">

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">repeatWeight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--repeat-weight"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getDouble</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedKmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--ordered-kmer-size"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getInteger</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedSketchSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--ordered-sketch-size"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getInteger</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">doReverseCompliment</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--no-rc"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getBoolean</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// read in the kmer filter set</span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="java">         <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">filterFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-f"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getString</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -339,10 +352,11 @@ public final class MhapMain</td>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxFraction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--filter-threshold"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getDouble</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removeUnique</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--supress-noise"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getInteger</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">noTf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--no-tf"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getBoolean</span><span class="o" style="font-weight: 600;">();</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="LC355" class="line" lang="java">                         <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--repeat-idf-scale"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getDouble</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="java">                 </span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="java">                         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">BufferedReader</span> <span class="n" style="color: #333;">bf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filterFile</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="java">                         <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC345" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FrequencyCounts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxFraction</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numThreads</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC359" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FrequencyCounts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxFraction</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numThreads</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">range</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="java">                 <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Exception</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -403,7 +417,10 @@ public final class MhapMain</td>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="java">                         </span>

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<td class="diff-line-num new_line" data-linenumber="418" style="width: 35px; color: rgba(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="LC418" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileList</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="419" style="width: 35px; color: rgba(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="LC419" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">cf</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fileList</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); 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="420" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC406" class="line" lang="java">                                         <span class="n" style="color: #333;">processFiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cf</span><span class="o" style="font-weight: 600;">);</span>                           </span>

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</td>

<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="java">                                         <span class="n" style="color: #333;">processFiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cf</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="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">

</td>

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

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

</pre>

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<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC422" class="line" lang="java">                         <span class="c1" style="color: #998; font-style: italic;">//sort the files in alphabetical order</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC423" class="line" lang="java">                         <span class="n" style="color: #333;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">processFiles</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

407

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<td class="diff-line-num new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

424

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

408

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

409

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<td class="diff-line-num new_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">

426

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">pf</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">processFiles</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); 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="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -537,7 +554,7 @@ public final class MhapMain</td>

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<td class="diff-line-num old_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<td class="diff-line-num new_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

554

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">MinHashSearch</span> <span class="nf" style="color: #900; font-weight: 600;">getMatchSearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SequenceSketchStreamer</span> <span class="n" style="color: #333;">hashStreamer</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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

<pre style="margin: 0;"> <span id="LC555" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC556" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hashStreamer</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numMinMatches</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numThreads</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</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="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

540

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<td class="diff-line-num new_line old" 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">

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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="LC540" class="line" lang="java">                         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minStoreLength</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">maxShift</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">acceptScore</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

557

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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="LC557" class="line" lang="java">                         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minStoreLength</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">maxShift</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">acceptScore</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</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

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<td class="diff-line-num new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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<pre style="margin: 0;"> <span id="LC558" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC559" class="line" lang="java"> </span>

</pre>

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<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

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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="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceSketchStreamer</span> <span class="nf" style="color: #900; font-weight: 600;">getSequenceHashStreamer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -547,7 +564,7 @@ public final class MhapMain</td>

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<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

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<td class="diff-line-num new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

564

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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="LC564" class="line" lang="java">                 <span class="n" style="color: #333;">seqStreamer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SequenceSketchStreamer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minOlapLength</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

548

</td>

<td class="diff-line-num new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

</td>

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

<pre style="margin: 0;"> <span id="LC565" class="line" lang="java">         <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

549

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<td class="diff-line-num new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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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="LC566" class="line" lang="java">                 <span class="n" style="color: #333;">seqStreamer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SequenceSketchStreamer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minOlapLength</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">numHashes</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="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="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">

</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="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">repeatWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</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="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">

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

<pre style="margin: 0;">+<span id="LC567" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedKmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedSketchSize</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="na" style="color: teal;">repeatWeight</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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

<pre style="margin: 0;"> <span id="LC568" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

552

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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="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqStreamer</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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553

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

<pre style="margin: 0;"> <span id="LC570" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<br>

</li>

<li id="148367d1edb07892fef68aa2439e944ddf44cd67">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#148367d1edb07892fef68aa2439e944ddf44cd67"><strong>src/main/java/edu/umd/marbl/mhap/sketch/BottomOverlapSketch.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +61,7 @@ public final class BottomOverlapSketch</td>

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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="LC61" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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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">

62

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></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">

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<td class="diff-line-num new_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">

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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="LC63" class="line" lang="java">  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

64

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<td class="diff-line-num new_line old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">p<span class="idiff left right">rivate</span></span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MatchData</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">

64

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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="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">p<span class="idiff left right">ublic</span></span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MatchData</span></span>

</pre>

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<td class="diff-line-num 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">

65

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<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="java">  <span class="o" style="font-weight: 600;">{</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="java">          <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">absMaxShiftInOverlap</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">          <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">;</span> </span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,7 +207,7 @@ public final class BottomOverlapSketch</td>

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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">

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="java">                         <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="java">                         <span class="o" style="font-weight: 600;">{</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">medianShift</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC210" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">absMaxShiftInOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seqLength1</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seqLength2</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="java">                                 <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">absMaxShiftInOverlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seqLength1</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seqLength2</span><span class="o" style="font-weight: 600;">)<span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java">                 </span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -274,6 +274,27 @@ public final class BottomOverlapSketch</td>

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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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<pre style="margin: 0;"> <span id="LC274" class="line" lang="java">                 </span>

</pre>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">valid</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</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="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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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java">         </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="278" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC278" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">matchesToString</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="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="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="java">         <span class="o" style="font-weight: 600;">{</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="280" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC280" class="line" lang="java">                 <span class="n" style="color: #333;">StringBuilder</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="java">                 <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"MatchData matches (size="</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">count</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"):\n"</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="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

282

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">count</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</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="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="283" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC283" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</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="284" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC284" class="line" lang="java">                         <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pos1Index</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pos2Index</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">posShift</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">"\n"</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="285" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC285" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</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="286" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC286" class="line" lang="java">                 </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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<pre style="margin: 0;">+<span id="LC287" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</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="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="288" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC288" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</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="289" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC289" class="line" lang="java"></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="290" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC290" class="line" lang="java">         <span class="cm" style="color: #998; font-style: italic;">/* (non-Javadoc)</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="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

291

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">              * @see java.lang.Object#toString()</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="292" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC292" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">              */</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="293" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC293" class="line" lang="java">         <span class="nd">@Override</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="294" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC294" class="line" lang="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">toString</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="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="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">

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</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="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC296" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"MatchData [count="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", shift="</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">getMedianShift</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>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</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="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">

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="java"> </span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -432,11 +453,63 @@ public final class BottomOverlapSketch</td>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="java">                         <span class="o" style="font-weight: 600;">{</span>                              </span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">//record match</span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="java">                                 <span class="n" style="color: #333;">matchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">recordMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pos1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pos2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">currShift</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="java"> </span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">// don't rely on repeats in the first iteration</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC437" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">repeat</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">//we need to create symmetry for reverse compliment, so we will look at first and last matches</span></span>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="java">                                 </span>

</pre>

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">//move the index to last point of same hash</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC460" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1Last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1</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="461" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC461" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i1Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC462" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i1Try</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC463" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC464" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hash1Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i1Try</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC465" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos1Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i1Try</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC466" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">hash1Try</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hash1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pos1Try</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">valid1Lower</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pos1Try</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">valid1Upper</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="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

467

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC468" class="line" lang="java">                                                 <span class="n" style="color: #333;">i1Last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1Try</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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469

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC470" class="line" lang="java">                                                 <span class="n" style="color: #333;">i1Try</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="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i1Try</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

472

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="java">                                                 </span>

</pre>

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474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="java">                                                 <span class="n" style="color: #333;">hash1Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i1Try</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="java">                                                 <span class="n" style="color: #333;">pos1Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i1Try</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>

</pre>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC478" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC479" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">//move the index to last point of same hash</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC480" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i2Last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2</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="481" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC481" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i2Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2</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>

</pre>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i2Try</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_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">

483

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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="LC483" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

484

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hash2Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i2Try</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos2Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i2Try</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

486

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">while</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">hash2Try</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hash2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pos2Try</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">valid2Lower</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pos2Try</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">valid2Upper</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="438" style="width: 35px; color: rgba(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="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

487

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

488

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="java">                                                 <span class="n" style="color: #333;">i2Last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2Try</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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

489

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<pre style="margin: 0;">+<span id="LC489" class="line" lang="java">                                                 <span class="n" style="color: #333;">i2Try</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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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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="LC490" class="line" lang="java">                                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i2Try</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="java">                                                         <span class="k" style="font-weight: 600;">break</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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="java">                                                 <span class="n" style="color: #333;">hash2Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i2Try</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="java">                                                 <span class="n" style="color: #333;">pos2Try</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i2Try</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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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="LC495" class="line" lang="java">                                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="java">                                 <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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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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="LC497" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="java">                                 <span class="c1" style="color: #998; font-style: italic;">//store the match and update the counters</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">i1Last</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">i2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">i2Last</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="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">{</span>              </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos1New</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">seq1KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i1Last</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="java">                                         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos2New</span> <span class="o" style="font-weight: 600;">=</span>  <span class="n" style="color: #333;">seq2KmerHashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i2Last</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(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="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="java">                                         <span class="n" style="color: #333;">matchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">recordMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pos1New</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pos2New</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pos2New</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pos1New</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="438" style="width: 35px; color: rgba(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="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="java">                                         <span class="n" style="color: #333;">i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i1Last</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="java">                                         <span class="n" style="color: #333;">i2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i2Last</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

506

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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="LC506" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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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="LC507" class="line" lang="java">                                 <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="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

508

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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="LC508" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="java">                                         <span class="c1" style="color: #998; font-style: italic;">//simply move on if they don't match</span></span>

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438

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<td class="diff-line-num new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="java">                                         <span class="n" style="color: #333;">i1</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="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

439

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<td class="diff-line-num new_line old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC439" class="line" lang="java">                                 <span class="n" style="color: #333;">i2</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="440" style="width: 35px; color: rgba(0,0,0,0.3); 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="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

511

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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="LC511" class="line" lang="java">                                         <span class="n" style="color: #333;">i2</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="440" style="width: 35px; color: rgba(0,0,0,0.3); 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="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC513" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_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">

441

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC514" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_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="diff-line-num new_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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC515" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); 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="522" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -449,7 +522,7 @@ public final class BottomOverlapSketch</td>

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC452" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">BottomOverlapSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sketchSize</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">BottomOverlapSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sketchSize</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seqLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmerSize</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>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -458,7 +531,7 @@ public final class BottomOverlapSketch</td>

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ZeroNGramsFoundException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Sequence length must be greater or equal to n-gram size "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="java">         </span>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// compute just direct hash of sequence</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">kmerSize</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">perm</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="java"></span>

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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="598" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -525,7 +598,8 @@ public final class BottomOverlapSketch</td>

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="java">         <span class="n" style="color: #333;">MatchData</span> <span class="n" style="color: #333;">matchData</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MatchData</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">toSequence</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxShiftPercent</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="java"></span>

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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">

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//get the initial matches</span></span>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="java">         <span class="n" style="color: #333;">recordMatchingKmers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">matchData</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">toSequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span>                     </span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="java">         <span class="n" style="color: #333;">recordMatchingKmers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">matchData</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">toSequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">orderedHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//System.out.println(matchData.matchesToString());</span></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="java">         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">matchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isEmpty</span><span class="o" style="font-weight: 600;">())</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OverlapInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">EMPTY</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="java"></span>

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<li id="1e41d87bd924d9b454d2e6a063050b66a4c558f7">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#1e41d87bd924d9b454d2e6a063050b66a4c558f7"><strong>src/main/java/edu/umd/marbl/mhap/sketch/BottomSketch.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -11,9 +11,9 @@ public class BottomSketch implements Sketch<BottomSketch></td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">       */</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">serialVersionUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9035607728472270206L</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">)</span></span>

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<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">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">BottomSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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

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<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">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); 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="16" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC16" class="line" lang="java">          <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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

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<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">

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<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">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java">          <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java">          </span>

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<br>

</li>

<li id="69fffa1e5dcd79efea80f6ce8db10a383eaf79c6">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#69fffa1e5dcd79efea80f6ce8db10a383eaf79c6"><strong>src/main/java/edu/umd/marbl/mhap/sketch/FrequencyCounts.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,17 +56,18 @@ public final class FrequencyCounts</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minValue</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_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="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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">range</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BloomFilter</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">validMers</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_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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<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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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">  </span>

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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">REPEAT_SCALE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">3.0</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java">  </span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">FrequencyCounts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">BufferedReader</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">filterCutoff</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">FrequencyCounts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">BufferedReader</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">filterCutoff</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">offset</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">range</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//removeUnique = 0: do nothing extra to k-mers not specified in the file</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//removeUnique = 1: remove k-mers not specified in the file from the sketch</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//removeUnique = 2: supress k-mers not specified in the file the same as max supression</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java">          </span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">range</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java">          </span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">removeUnique</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">removeUnique</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>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java">                  <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">MhapRuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown removeUnique option "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">removeUnique</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>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java">          </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -78,7 +79,7 @@ public final class FrequencyCounts</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java">          <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">noTf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">noTf</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">          </span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// generate hashset</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java">          <span class="n" style="color: #333;">Long2DoubleOpenHashMap</span> <span class="n" style="color: #333;">validMap</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Long2DoubleOpenHashMap</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java">          <span class="n" style="color: #333;">Long2DoubleOpenHashMap</span> <span class="n" style="color: #333;">validMap</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java">          <span class="n" style="color: #333;">BloomFilter</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">validMers</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//the max value observed in the list</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -88,29 +89,52 @@ public final class FrequencyCounts</td>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java">          <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readLine</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java">          <span class="k" style="font-weight: 600;">try</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">sizeBloom</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java">                  <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">sizeRepeat</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java">                  <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">                  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java">                          <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Warning, k-mer filter file is empty. Assuming zero entries."</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java">                          <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java">                          <span class="n" style="color: #333;">size<span class="idiff left">Bloom</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">sizeRepeat</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">                  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">                  <span class="k" style="font-weight: 600;">else</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">

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</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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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java">                          <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</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="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="java">                         <span class="c1" style="color: #998; font-style: italic;">// we assume the line has two entries, the first is the size of the bloom filter, the second is the size of the filter set</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="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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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java">                         <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">splitLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">trim</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">split</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\s+"</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="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">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java">                         <span class="n" style="color: #333;">sizeBloom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitLine</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>

</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">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">                         <span class="n" style="color: #333;">sizeRepeat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitLine</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>

</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="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="java">                         <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Read in values for repeat "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sizeRepeat</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" and "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sizeBloom</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java">                 </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="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">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0L</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="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="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="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size<span class="idiff left">Bloom</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="mi" style="color: #099;"><span class="idiff">0L</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">sizeRepeat</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0L</span><span class="o" style="font-weight: 600;">)</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="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">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">MhapRuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"K-mer filter file size line must have positive long value."</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java">                         <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="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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<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="LC104" class="line" lang="java">                         <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0L</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="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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<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="java">                         <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">size<span class="idiff left right">Bloom</span></span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0L</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="java">                         <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="java">                                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Warning, k-mer filter file has zero elements."</span><span class="o" style="font-weight: 600;">);</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="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="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">

</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="LC107" class="line" lang="java">                                 <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">;</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="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">

</td>

<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">

113

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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="LC113" class="line" lang="java">                                 <span class="n" style="color: #333;">size<span class="idiff left right">Bloom</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1L</span><span class="o" style="font-weight: 600;">;</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="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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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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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="LC114" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</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="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<td class="diff-line-num new_line" data-linenumber="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="java">                 <span class="o" style="font-weight: 600;">}</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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="diff-line-num new_line" data-linenumber="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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC116" class="line" lang="java">                 </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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC117" class="line" lang="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Initializing"</span><span class="o" style="font-weight: 600;">);</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="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">

</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="java">                 <span class="n" style="color: #333;">Long2DoubleOpenHashMap</span> <span class="n" style="color: #333;">tempMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</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="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">

</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="java">                 <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sizeRepeat</span><span class="o" style="font-weight: 600;">;</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="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</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="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">

</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="java">                         <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</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="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">

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

<pre style="margin: 0;">+<span id="LC121" class="line" lang="java">                                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Trying size "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<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="java">                                 <span class="n" style="color: #333;">tempMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Long2DoubleOpenHashMap</span><span class="o" style="font-weight: 600;">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC123" class="line" lang="java">                                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" and it was successfull"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC124" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</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="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">

</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="java">                         <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">IllegalArgumentException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC126" class="line" lang="java">                                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" and it was too big, trying smaller"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC127" class="line" lang="java">                         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tempMap</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</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="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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<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">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java">                         <span class="n" style="color: #333;">validMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Long2DoubleOpenHashMap</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="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">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java">                 <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="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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<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">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java">                         <span class="n" style="color: #333;">validMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempMap</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="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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<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="java">                 <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Initialized"</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="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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<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="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java">                 <span class="c1" style="color: #998; font-style: italic;">//if no nothing, no need to store the while list</span></span>

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

</pre>

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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">

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java">                         <span class="n" style="color: #333;">validMers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BloomFilter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">create</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sink</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sink</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">putLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_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">

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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="java">                         <span class="n" style="color: #333;">validMers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BloomFilter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">create</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sink</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">sink</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">putLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">size<span class="idiff left right">Bloom</span></span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="java">                 <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java">                         <span class="n" style="color: #333;">validMers</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,7 +166,7 @@ public final class FrequencyCounts</td>

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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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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java">                                         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">kmerSizes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">}</span>                                      </span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java">                                 </span>

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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">

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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="LC145" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">(),</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java">                                 <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">(),</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(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="LC170" class="line" lang="java">                                 </span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java">                                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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>

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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="LC172" class="line" lang="java">                                 <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -265,7 +289,7 @@ public final class FrequencyCounts</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">scaledIdf</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">)</span></span>

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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="LC291" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); 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="292" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC268" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">scaledIdf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">REPEAT_SCALE</span></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="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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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC292" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">scaledIdf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">range</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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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="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(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="LC294" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_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">

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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="LC295" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">scaledIdf</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxValue</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<br>

</li>

<li id="ff6aa275e4b4c1fa06704090afb1c5cafaaea820">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#ff6aa275e4b4c1fa06704090afb1c5cafaaea820"><strong>src/main/java/edu/umd/marbl/mhap/sketch/HashUtils.java</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="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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,7 @@ import com.google.common.hash.Hashing;</td>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">edu.umd.marbl.mhap.math.BasicMath</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">edu.umd.marbl.mhap.utils.MersenneTwisterFast</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">edu.umd.marbl.mhap.utils.Utils</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">HashUtils</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"><span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,7 +158,7 @@ public class HashUtils</td>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">computeNGramHashes</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">computeNGramHashes</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numberNGrams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()-</span><span class="n" style="color: #333;">nGramSize</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>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> </span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -165,7 +166,7 @@ public class HashUtils</td>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java">                 <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">SketchRuntimeException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"N-gram size bigger than string length."</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> </span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">// get the rabin hashes</span></span>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rabinHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rabinHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java">         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rabinHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java"> </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">@@ -209,28 +210,47 @@ public class HashUtils</td>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">computeSequenceHashes</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="java">         <span class="n" style="color: #333;">HashFunction</span> <span class="n" style="color: #333;">hf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">murmur3_32</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="java"> </span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nGramSize</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>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">++)</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java">                 <span class="n" style="color: #333;">HashCode</span> <span class="n" style="color: #333;">hc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newHasher</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">putUnencodedChars</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: teal;">hash</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">strReverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java">                         <span class="n" style="color: #333;">strReverse</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">rc</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_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">

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">strReverse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">)<</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java">                                 <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strReverse</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="java">                 <span class="n" style="color: #333;">HashCode</span> <span class="n" style="color: #333;">hc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newHasher</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">putUnencodedChars</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">hash</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="java">                 <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">asInt</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC237" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kd" style="font-weight: 600;"><span class="idiff">final</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="228" style="width: 35px; color: rgba(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="LC239" class="line" lang="java">         <span class="n" style="color: #333;">HashFunction</span> <span class="n" style="color: #333;">hf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Hashing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">murmur3_128</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seed</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="java"> </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">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="java">         <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nGramSize</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>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">++)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="java">                 <span class="n" style="color: #333;">HashCode</span> <span class="n" style="color: #333;">hc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newHasher</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">putUnencodedChars</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: teal;">hash</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">substring</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">strReverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">doReverseCompliment</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java">                         <span class="n" style="color: #333;">strReverse</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">rc</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="java">                         <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">strReverse</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">)<</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java">                                 <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strReverse</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="java">                 </span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java">                 <span class="n" style="color: #333;">HashCode</span> <span class="n" style="color: #333;">hc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newHasher</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">putUnencodedChars</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">hash</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="java">                 <span class="n" style="color: #333;">hashes</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hc</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">asLong</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="java"> </span>

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<br>

</li>

<li id="bc59179d9c4f81f60f7286c877f4f65d3072327b">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#bc59179d9c4f81f60f7286c877f4f65d3072327b"><strong>src/main/java/edu/umd/marbl/mhap/sketch/MinHashBitSketch.java</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="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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,9 +75,9 @@ public final class MinHashBitSketch extends AbstractBitSketch<MinHashBitSketch></td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getAsBits</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minHashes</span><span class="o" style="font-weight: 600;">));</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java">  </span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashBitSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashBitSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getAsBits</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">()));</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java">          <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getAsBits</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numWords</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getMinHashArray</span><span class="o" style="font-weight: 600;">()));</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">  </span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">jaccard</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">MinHashBitSketch</span> <span class="n" style="color: #333;">sh</span><span class="o" style="font-weight: 600;">)</span></span>

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<br>

</li>

<li id="56e3977de1abb5faadbbd6204900ae0f13504014">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#56e3977de1abb5faadbbd6204900ae0f13504014"><strong>src/main/java/edu/umd/marbl/mhap/sketch/MinHashSketch.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); 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="49" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -49,7 +49,7 @@ public final class MinHashSketch implements Sketch<MinHashSketch></td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">serialVersionUID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8846482698636860862L</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java">  </span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java">  <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">computeNgramMinHashesWeighted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java">                  <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java">                  <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">kmerFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java">          <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numberNGrams</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nGramSize</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>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">  </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">@@ -60,7 +60,7 @@ public final class MinHashSketch implements Sketch<MinHashSketch></td>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//  throw new SketchRuntimeException("repeatWeight cannot be >=1.");</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">// get the kmer hashes</span></span>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java">          <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">kmerHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java">          <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">kmerHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HashUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeSequenceHashesLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java">          </span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java">          <span class="c1" style="color: #998; font-style: italic;">//now compute the counts of occurance</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">          <span class="n" style="color: #333;">Long2ObjectLinkedOpenHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">HitCounter</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">hitMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Long2ObjectLinkedOpenHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">HitCounter</span><span class="o" style="font-weight: 600;">>(</span><span class="n" style="color: #333;">kmerHashes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -205,14 +205,14 @@ public final class MinHashSketch implements Sketch<MinHashSketch></td>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minHashes</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="java"> </span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

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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="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">doReverseCompliment</span></span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeNgramMinHashesWeighted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</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="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeNgramMinHashesWeighted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java"> </span>

</pre>

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<td class="diff-line-num old old_line" 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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<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="LC213" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">freqFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">MinHashSketch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FrequencyCounts</span> <span class="n" style="color: #333;">freqFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">ZeroNGramsFoundException</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="214" style="width: 35px; color: rgba(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="LC214" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); 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="215" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC215" class="line" lang="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeNgramMinHashesWeighted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">freqFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">repeatWeight</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="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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<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="java">         <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">minHashes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MinHashSketch</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">computeNgramMinHashesWeighted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nGramSize</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numHashes</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">freqFilter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">doReverseCompliment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">repeatWeight</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(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="LC216" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">getAsByteArray</span><span class="o" style="font-weight: 600;">()</span></span>

</pre>

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<br>

</li>

<li id="1a74da5211d7ca610f86db293745349b5150cf22">

<a href="https://salsa.debian.org/med-team/mhap/compare/78207da2ebb99aa68b63b9209835c7138aab225f...ef042b49e04879970d8537a1ef7c967f59f3f67f#1a74da5211d7ca610f86db293745349b5150cf22"><strong>src/main/java/edu/umd/marbl/mhap/utils/Utils.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); 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="33" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -33,6 +33,7 @@ import java.text.DecimalFormat;</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.NumberFormat</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Map</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Random</span><span class="o" style="font-weight: 600;">;</span></span>

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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="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.BufferedInputStream</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.BufferedReader</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="45" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -44,10 +45,12 @@ import java.io.FileReader;</td>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); 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="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC48" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">it.unimi.dsi.fastutil.objects.Object2ObjectOpenHashMap</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC49" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Utils</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC50" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ToProtein</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kd" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ToProtein</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">          <span class="n" style="color: #333;">AAA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AAC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AAG</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AAT</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ACA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ACC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ACG</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ACT</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AGA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AGC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AGG</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">AGT</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">                          <span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ATA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"I"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ATC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"I"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ATG</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"M"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">ATT</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"I"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CAA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Q"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CAC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CAG</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Q"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CAT</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CCA</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"P"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CCC</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"P"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">CCG</span><span class="o" style="font-weight: 600;">(</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">@@ -78,22 +81,39 @@ public final class Utils</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;"><span class="idiff left right">enum</span></span> <span class="n" style="color: #333;">Translate</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java">  <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff"> </span><span class="kd" style="font-weight: 600;"><span class="idiff right">class</span></span> <span class="nc" style="color: #458; font-weight: 600;">Translate</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java">  <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java">          <span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">B</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"V"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"G"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"H"</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="s" style="color: #d14;">"C"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">H</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"D"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">K</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"M"</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="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">R</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Y"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">V</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"B"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">W</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"W"</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">Y</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java">                          <span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">);</span></span>

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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="LC85" class="line" lang="java"></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="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">

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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="LC86" class="line" lang="java">          <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">other</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="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="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">

</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="LC87" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

88

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<td class="diff-line-num new_line old" 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">

</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="LC88" class="line" lang="java">          <span class="n" style="color: #333;">Translate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">other</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="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">

89

</td>

<td class="diff-line-num new_line old" 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">

</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="LC89" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</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

</td>

<td class="diff-line-num new_line old" 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">

</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="LC90" class="line" lang="java">                  <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">          <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lookup</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Object2ObjectOpenHashMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">String</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="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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<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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC87" class="line" lang="java">          </span>

</pre>

</td>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_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">

88

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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="LC88" class="line" lang="java">          <span class="kd" style="font-weight: 600;">static</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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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<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">

89

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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="LC89" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</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="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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<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">

90

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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="LC90" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"T"</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="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">

</td>

<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">

91

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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="LC91" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"B"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"V"</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="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">

</td>

<td class="diff-line-num new new_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">

92

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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="LC92" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"C"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"G"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<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">

93

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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="LC93" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"D"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<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">

94

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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="LC94" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"G"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"C"</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="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">

</td>

<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">

95

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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="LC95" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"H"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"D"</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="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">

</td>

<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">

96

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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="LC96" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"M"</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="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">

</td>

<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">

97

</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="LC97" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"K"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

</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="LC98" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<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">

99

</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="LC99" class="line" lang="java">                  <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Y"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<td class="diff-line-num new new_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">

100

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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="LC100" class="line" lang="java">                 <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"S"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC101" class="line" lang="java">                 <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"T"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"A"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC102" class="line" lang="java">                 <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"V"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"B"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC103" class="line" lang="java">                 <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"W"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"W"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">                 <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Y"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"R"</span><span class="o" style="font-weight: 600;">);</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="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">

</td>

<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">

105

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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="LC105" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC106" class="line" lang="java">         </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="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">

</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="java">         <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getTranslation</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">)</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="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">

</td>

<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

</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="LC108" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</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="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">

</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="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC110" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</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="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">

</td>

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

<pre style="margin: 0;">+<span id="LC111" class="line" lang="java">                         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">;</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="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">

</td>

<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">

112

</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="LC112" class="line" lang="java">                 </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="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">

</td>

<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">

113

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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="LC113" class="line" lang="java">                 <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</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="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">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"></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="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="java">          <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getCompliment</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="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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<td class="diff-line-num new_line old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC94" class="line" lang="java">          <span class="o" style="font-weight: 600;">{</span></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="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="java">                  <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">other</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="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="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="java">          <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="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">

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java">         <span class="c1" style="color: #998; font-style: italic;">//A("T"), B("V"), C("G"), D("H"), G("C"), H("D"), K("M"), M("K"), N("N"), R("Y"), S("S"), T("A"), V("B"), W("W"), Y("R");</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</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">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="java"></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">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BUFFER_BYTE_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8388608</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// 8MB</span></span>

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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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -479,16 +499,9 @@ public final class Utils</td>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="java">         <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">supplied</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</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="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--)</span></span>

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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="500" style="width: 35px; color: rgba(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="LC500" class="line" lang="java">         <span class="o" style="font-weight: 600;">{</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">

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<td class="diff-line-num new_line" data-linenumber="501" style="width: 35px; color: rgba(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="LC501" class="line" lang="java">                 <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">theChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">supplied</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>

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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">

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<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); 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="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); 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="502" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC483" class="line" lang="java">                 <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">theChar</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'-'</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="484" style="width: 35px; color: rgba(0,0,0,0.3); 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="502" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC484" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC485" class="line" lang="java">                         <span class="n" style="color: #333;">Translate</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Translate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">theChar</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">toUpperCase</span><span class="o" style="font-weight: 600;">());</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="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

486

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC486" class="line" lang="java">                         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCompliment</span><span class="o" style="font-weight: 600;">());</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="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

487

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC487" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</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="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

488

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC488" class="line" lang="java">                 <span class="k" style="font-weight: 600;">else</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="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

489

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC489" class="line" lang="java">                 <span class="o" style="font-weight: 600;">{</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="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

490

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC490" class="line" lang="java">                         <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</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>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

491

</td>

<td class="diff-line-num new_line old" data-linenumber="502" style="width: 35px; color: rgba(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="LC491" class="line" lang="java">                 <span class="o" style="font-weight: 600;">}</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="492" style="width: 35px; color: rgba(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="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

</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="LC502" class="line" lang="java">                 </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="492" style="width: 35px; color: rgba(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="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

</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="LC503" class="line" lang="java">                 <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Translate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getTranslation</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">Character</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">theChar</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">toUpperCase</span><span class="o" style="font-weight: 600;">()));</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="492" style="width: 35px; color: rgba(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="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

</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="LC504" class="line" lang="java">                 <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

492

</td>

<td class="diff-line-num new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

</td>

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

<pre style="margin: 0;"> <span id="LC505" class="line" lang="java">         <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

</td>

<td class="diff-line-num new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

</td>

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

<pre style="margin: 0;"> <span id="LC506" class="line" lang="java">         <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

</td>

</tr>

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

<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

</td>

<td class="diff-line-num new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

507

</td>

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

<pre style="margin: 0;"> <span id="LC507" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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