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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/fastqc">Debian Med / fastqc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381">d1c9f051</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-01-12T22:40:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.9+dfsg</pre>
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<h4>16 changed files:</h4>
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<li class="file-stats">
<a href="#4fdb66e9a71290900c394c06ea3c24269a49d914">
Help/3 Analysis Modules/12 Per Tile Sequence Quality.html
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<li class="file-stats">
<a href="#7cfedbc97673f872cd1f9bdd3bdd2509acdbe496">
INSTALL.txt
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<li class="file-stats">
<a href="#7218c513d6f727b5ea96fc048c04738db1285799">
RELEASE_NOTES.txt
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<li class="file-stats">
<a href="#3298ccc787ae057230815e840c980c07cee031f3">
fastqc
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<li class="file-stats">
<a href="#e441b0d7320c3d27b019e0c2123f17909e0539c5">
uk/ac/babraham/FastQC/Analysis/AnalysisRunner.java
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<li class="file-stats">
<a href="#84fff692b48938cf047014dc655e47eccf9f4c11">
uk/ac/babraham/FastQC/Analysis/OfflineRunner.java
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<li class="file-stats">
<a href="#4abecb201fc238d51df86967669e9721b0b19f86">
uk/ac/babraham/FastQC/FastQCApplication.java
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<li class="file-stats">
<a href="#e9f63f51554c886d766c4f8514ac17292120173c">
uk/ac/babraham/FastQC/Graphs/LineGraph.java
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<li class="file-stats">
<a href="#46343b9eab75ba9806dd1e6132091498ce2ff3bf">
uk/ac/babraham/FastQC/Modules/AdapterContent.java
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<li class="file-stats">
<a href="#2f80f99e3f19d949f693ab40702d4730e21cd809">
uk/ac/babraham/FastQC/Modules/BasicStats.java
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<li class="file-stats">
<a href="#599886f55ff6b2afb619da338a48b076cd60db4b">
uk/ac/babraham/FastQC/Modules/DuplicationLevel.java
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<li class="file-stats">
<a href="#ff73039d6f80221ab4399063f3ba9f2bc2a7017a">
uk/ac/babraham/FastQC/Modules/PerTileQualityScores.java
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<li class="file-stats">
<a href="#c374db931477fae930a0a924ef5dec32c2a7cd32">
uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.java
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<li class="file-stats">
<a href="#3013cb0481f38b744114f30dd2156d353af7ebf7">
uk/ac/babraham/FastQC/Results/ResultsPanel.java
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<li class="file-stats">
<a href="#b814303178e7f8f116f1ffd8cc7f1791e501935b">
uk/ac/babraham/FastQC/Sequence/Fast5File.java
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<li class="file-stats">
<a href="#b07e05b73f29161440c9490fa2d0a5ee9e032c8e">
uk/ac/babraham/FastQC/Utilities/NanoporeBasename.java
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</ul>
<h4>Changes:</h4>
<li id="4fdb66e9a71290900c394c06ea3c24269a49d914">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#4fdb66e9a71290900c394c06ea3c24269a49d914"><strong>Help/3 Analysis Modules/12 Per Tile Sequence Quality.html</strong></a>
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<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">@@ -45,7 +45,7 @@ tiles.</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="html"></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="html"><span class="nt" style="color: #000080;"><h2></span>Failure<span class="nt" style="color: #000080;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span></span>
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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC48" class="line" lang="html">This module will <span class="idiff left right">issue a warning</span> if any tile shows a mean Phred</span>
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<td class="diff-line-num new old_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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<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="html">This module will <span class="idiff left right">raise and error</span> if any tile shows a mean Phred</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="html">score more than 5 less than the mean for that base across all</span>
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<td class="diff-line-num old_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">
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="html">tiles. </span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="html"><span class="nt" style="color: #000080;"></p></span></span>
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<li id="7cfedbc97673f872cd1f9bdd3bdd2509acdbe496">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#7cfedbc97673f872cd1f9bdd3bdd2509acdbe496"><strong>INSTALL.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Installing FastQC</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">-------------------</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">FastQC is a java application. In order to run it needs your system to have a suitable</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Java Runtime Environment (JRE) installed. Before you try to run FastQC you should therefore</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">ensure that you have a suitable JRE. There are a number of different JREs available</span>
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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">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">however the ones we have tested are the v1.6-v1.8 JREs from Oracle. These are available</span>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">for a number of different platforms.</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Windows/Linux: Go to java.com - click on Free Java Download - DON'T click the large red button</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">but choose the smaller link to "See all java downloads". Find your operating system and select</span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">the appropriate offline installer. If you are using a 64bit operating system (and nearly </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">everyone is these days), then make sure you select the 64bit version of the the installer.</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">OSX: On newer versions of OSX you need to install the Java Development Kit. The normal Java</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">runtime environment IS NOT enough. To get this go to java.com, click "Free java download",</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">then IGNORE the big red button, and select "See all java downloads", on the next screen select</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">"Looking for the JDK?" from the left hand menu and select the link to "JDK downloads" in the</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">first paragraph. You can then click the "Download" button underneath JDK in the page you are</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">taken to. Sorry this is such a pain!</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">If you're not sure whether you have java installed then you can test this from a command</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">prompt. To get a command prompt try:</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Windows: Select Start > Run, and type 'cmd' (no quotes) in the box which appears, press OK</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">MaxOSX: Run Applications > Utilities > Terminal</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Linux: From your applications menu look for an application called 'Terminal' or 'Konsole'.</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Either of these will give you a usable shell.</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">At the command prompt type 'java -version' and press enter. You should see something like:</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">java version "1.8.0_60"</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Java(TM) SE Runtime Environment (build 1.8.0_60-b27)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">If you get an error then you don't have java installed. If the version listed on the first</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">line is less than 1.6 then you might have problems running FastQC.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Actually installing FastQC is as simple as unzipping the zip file it comes in into a</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">suitable location. That's it. Once unzipped it's ready to go.</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">Running FastQC</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">--------------</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">You can run FastQC in one of two modes, either as an interactive graphical application</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">in which you can dynamically load FastQ files and view their results.</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">Alternatively you can run FastQC in a non-interactive mode where you specify the files</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">you want to process on the command line and FastQC will generate an HTML report for</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">each file without launching a user interface. This would allow FastQC to be run as</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">part of an analysis pipeline.</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">Running FastQC Interactively</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">----------------------------</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">Windows: Simply double click on the run_fastqc bat file. If you want to make a pretty </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">shortcut then we've included an icon file in the top level directory so you don't have</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">to use the generic bat file icon.</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">MacOSX: There is an application bundle for MacOSX which you can use to install and run</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">FastQC. Just drag the application from the disk image to your Applications folder (or</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">wherever you want to install the program).</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">Linux: We have included a wrapper script, called 'fastqc' which is the easiest way to </span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">start the program. The wrapper is in the top level of the FastQC installation. You </span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">may need to make this file executable:</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">chmod 755 fastqc</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">..but once you have done that you can run it directly</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">./fastqc</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">..or place a link in /usr/local/bin to be able to run the program from any location:</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">Running FastQC as part of a pipeline</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">------------------------------------</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">To run FastQC non-interactively you should use the fastqc wrapper script to launch</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">the program. You will probably want to use the zipped install file on every platform</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext">(even OSX).</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">To run non-interactively you simply have to specify a list of files to process</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">on the commandline</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">fastqc somefile.txt someotherfile.txt</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">You can specify as many files to process in a single run as you like. If you don't</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">specify any files to process the program will try to open the interactive application</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">which may result in an error if you're running in a non-graphical environment.</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">There are a few extra options you can specify when running non-interactively. Full</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">details of these can be found by running </span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">fastqc --help</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">By default, in non-interactive mode FastQC will create an HTML report with embedded</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">graphs, but also a zip file containing individual graph files and additional data files</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">containing the raw data from which plots were drawn. The zip file will not be extracted</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">by default but you can enable this by adding:</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">--extract</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">To the launch command.</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">If you want to save your reports in a folder other than the folder which contained</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">your original FastQ files then you can specify an alternative location by setting a</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">--outdir value:</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">--outdir=/some/other/dir/</span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">If you want to run fastqc on a stream of data to be read from standard input then you</span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">can do this by specifing 'stdin' as the name of the file to be processed and then </span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">streaming uncompressed fastq format data to the program. For example:</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">zcat *fastq.gz | fastqc stdin</span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">If you want the results from a streamed analysis sent to a file with a name other than</span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">stdin then you can add a colon and put the file name you want, for example:</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">zcat *fastq.gz | fastqc stdin:my_results</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">..would write results to my_result.html and my_results.zip.</span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">Customising the report output</span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">-----------------------------</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">If you want to run FastQC as part of a sequencing pipeline you may wish to change the</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">formatting of the report to add in your own branding or to include extra information.</span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">In the Templates directory you will find a file called 'header_template.html' which</span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">you can edit to change the look of the report. This file contains all of the header for</span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">the report file, including the CSS section and you can alter this however you see fit.</span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext">Whilst you can make whatever changes you like you should probably leave in place the</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"><div> structure of the html template since later code will expect to close the main div</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">which is left open at the end of the header. There is no facility to change the code in</span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">the main body of the report or the footer (although you can of course change the styling).</span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext">report it created. You can use these placeholders in other parts of the header if you</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">wish.</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Installing FastQC</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">-------------------</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">OSX</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">---</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">FastQC is distributed as a DMG image file. Download the image from the project page</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">and double click it to open it. You should see the FastQC application appear in a</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Finder window. Drag the application from there to wherever you want to install it </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">on your machine. Once you've copied the application double click it to open it.</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">FastQC is not a signed application therefore it may initially be blocked by the</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Gatekeeper application. To avoid this open FastQC by right clicking on the app </span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">and selecting open. This may prompt you to allow it to open. If it is still </span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">blocked go to System Preferences > Security and Privacy and you should see an option</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">to allow the application to open. You only need to do this once and the preference</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">should be remembered by OSX.</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Windows and Linux</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">-----------------</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">FastQC is a java application. In order to run it needs your system to have a suitable</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Java Runtime Environment (JRE) installed. Before you try to run FastQC you should </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">therefore ensure that you have a suitable JRE. There are a number of different JREs </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">available however the ones we have tested are the latest Oracle runtime environments </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">and those from the adoptOpenJDK project (https://adoptopenjdk.net/). You need to </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">download and install a suitable 64-bit JRE and make sure that the java application </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">is in your path (most installers will take care of this for you).</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">On linux most distributions will have java installed already so you might not need to</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">do anything. If java isn't installed then you can add it by doing:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Ubuntu / Mint: sudo apt install default-jre</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">CentOS / Redhat: sudo yum install java-1.8.0-openjdk</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">You can check whether java is installed by opening the 'cmd' program on windows, or</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">any shell on linux and typing:</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">java -version</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">You should see something like:</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">>java -version</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">openjdk version "11.0.2" 2019-01-15</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Actually installing FastQC is as simple as unzipping the zip file it comes in into a</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">suitable location. That's it. Once unzipped it's ready to go.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Running FastQC</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">--------------</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">You can run FastQC in one of two modes, either as an interactive graphical application</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">in which you can dynamically load FastQ files and view their results.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Alternatively you can run FastQC in a non-interactive mode where you specify the files</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">you want to process on the command line and FastQC will generate an HTML report for</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">each file without launching a user interface. This would allow FastQC to be run as</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">part of an analysis pipeline.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Running FastQC Interactively</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">----------------------------</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Windows: Simply double click on the run_fastqc bat file. If you want to make a pretty </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">shortcut then we've included an icon file in the top level directory so you don't have</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">to use the generic bat file icon.</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">MacOSX: Double click on the FastQC application icon.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Linux: We have included a wrapper script, called 'fastqc' which is the easiest way to </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">start the program. The wrapper is in the top level of the FastQC installation. You </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">may need to make this file executable:</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">chmod 755 fastqc</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">..but once you have done that you can run it directly</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">./fastqc</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">..or place a link in /usr/local/bin to be able to run the program from any location:</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">sudo ln -s /path/to/FastQC/fastqc /usr/local/bin/fastqc</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">Running FastQC as part of a pipeline</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">------------------------------------</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">To run FastQC non-interactively you should use the fastqc wrapper script to launch</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">the program. You will probably want to use the zipped install file on every platform</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">(even OSX).</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">To run non-interactively you simply have to specify a list of files to process</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">on the commandline</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">fastqc somefile.txt someotherfile.txt</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">You can specify as many files to process in a single run as you like. If you don't</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">specify any files to process the program will try to open the interactive application</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">which may result in an error if you're running in a non-graphical environment.</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">There are a few extra options you can specify when running non-interactively. Full</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">details of these can be found by running </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">fastqc --help</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">By default, in non-interactive mode FastQC will create an HTML report with embedded</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">graphs, but also a zip file containing individual graph files and additional data files</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">containing the raw data from which plots were drawn. The zip file will not be extracted</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">by default but you can enable this by adding:</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">--extract</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">To the launch command.</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">If you want to save your reports in a folder other than the folder which contained</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">your original FastQ files then you can specify an alternative location by setting a</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">--outdir value:</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">--outdir=/some/other/dir/</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">If you want to run fastqc on a stream of data to be read from standard input then you</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">can do this by specifing 'stdin' as the name of the file to be processed and then </span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">streaming uncompressed fastq format data to the program. For example:</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">zcat *fastq.gz | fastqc stdin</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">If you want the results from a streamed analysis sent to a file with a name other than</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">stdin then you can add a colon and put the file name you want, for example:</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">zcat *fastq.gz | fastqc stdin:my_results</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">..would write results to my_result.html and my_results.zip.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Customising the report output</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">-----------------------------</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">If you want to run FastQC as part of a sequencing pipeline you may wish to change the</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">formatting of the report to add in your own branding or to include extra information.</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">In the Templates directory you will find a file called 'header_template.html' which</span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">you can edit to change the look of the report. This file contains all of the header for</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">the report file, including the CSS section and you can alter this however you see fit.</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">Whilst you can make whatever changes you like you should probably leave in place the</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"><div> structure of the html template since later code will expect to close the main div</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">which is left open at the end of the header. There is no facility to change the code in</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">the main body of the report or the footer (although you can of course change the styling).</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the</span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">report it created. You can use these placeholders in other parts of the header if you</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">wish.</span></pre>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#7218c513d6f727b5ea96fc048c04738db1285799"><strong>RELEASE_NOTES.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">RELEASE NOTES FOR FastQC v0.11.9</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">--------------------------------</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">This is a bugfix release which resolves some issues with the program;</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- We removed the native look and feel from the linux application since</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> it's horribly broken</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">- Fixed a hang if a run terminated from an out-of-memory error</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- Fixed a corner case where adapters could occasionally be double-counted</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Updated the fast5 parser to account for the newer format multi-read</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> oxford nanopore fast5 files</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Fixed problems if analysing a completely blank file</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">RELEASE NOTES FOR FastQC v0.11.8</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">--------------------------------</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<li id="3298ccc787ae057230815e840c980c07cee031f3">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#3298ccc787ae057230815e840c980c07cee031f3"><strong>fastqc</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">@@ -45,6 +45,29 @@ else {</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ENV</span><span class="p">{</span><span class="nv" style="color: #008080;">CLASSPATH</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin$delimiter$RealBin</span><span class="s2" style="color: #d14;">/sam-1.103.jar</span><span class="si" style="color: #d14;">$delimiter$RealBin</span><span class="s2" style="color: #d14;">/jbzip2-0.9.jar</span><span class="si" style="color: #d14;">$delimiter$RealBin</span><span class="s2" style="color: #d14;">/cisd-jhdf5.jar</span><span class="p">";</span></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="perl"><span class="p">}</span></span>
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47
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># We need to find the java interpreter. We'll start from the assumption that this</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># is included in the path.</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$java_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">java</span><span class="p">";</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># We might have bundled a jre with the installation. If that's the case then we'll</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># use the interpreter which is bundled in preference to the system one.</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Windows first</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/bin/java.exe</span><span class="p">")</span> <span class="p">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"> <span class="nv" style="color: #008080;">$java_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/bin/java.exe</span><span class="p">";</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"><span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Linux</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/bin/java</span><span class="p">")</span> <span class="p">{</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"> <span class="nv" style="color: #008080;">$java_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/bin/java</span><span class="p">";</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"><span class="p">}</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># OSX</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/Contents/Home/bin/java</span><span class="p">")</span> <span class="p">{</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"> <span class="nv" style="color: #008080;">$java_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$RealBin</span><span class="s2" style="color: #d14;">/jre/Contents/Home/bin/java</span><span class="p">";</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="p">}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"></span>
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48
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@java_args</span><span class="p">;</span></span>
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49
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@files</span><span class="p">;</span></span>
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50
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"></span>
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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="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -79,7 +102,6 @@ my $nano;</td>
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79
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$nofilter</span><span class="p">;</span></span>
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80
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$kmer_size</span><span class="p">;</span></span>
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81
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$temp_directory</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$java_bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">java</span><span class="p">';</span></span>
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83
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$min_length</span><span class="p">;</span></span>
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84
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="perl"></span>
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85
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">GetOptions</span><span class="p">('</span><span class="s1" style="color: #d14;">version</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">$version</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -234,6 +256,8 @@ if ($format) {</td>
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234
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="perl"><span class="p">}</span></span>
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235
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="perl"></span>
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236
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$java_bin</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">'</span><span class="s1" style="color: #d14;">java</span><span class="p">')</span> <span class="p">{</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">warn</span> <span class="p">"</span><span class="s2" style="color: #d14;">Java is </span><span class="si" style="color: #d14;">$java_bin</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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237
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># $java_bin =~ s/\\/\//g;</span></span>
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238
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="perl"> </span>
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239
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$java_bin</span><span class="p">)</span> <span class="p">{</span></span>
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<li id="e441b0d7320c3d27b019e0c2123f17909e0539c5">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#e441b0d7320c3d27b019e0c2123f17909e0539c5"><strong>uk/ac/babraham/FastQC/Analysis/AnalysisRunner.java</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Analysis</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="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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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFormatException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC31" 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;">AnalysisRunner</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Runnable</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</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="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</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="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">listeners</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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;">percentComplete</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="LC37" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">AnalysisRunner</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</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="LC39" 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: #008080;">file</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>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addAnalysisListener</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span> <span class="n" style="color: #333;">l</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="LC43" 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;">l</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="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</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="LC44" class="line" lang="java"> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">removeAnalysisListener</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span> <span class="n" style="color: #333;">l</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="LC49" 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;">l</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;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</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="LC50" class="line" lang="java"> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">startAnalysis</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" 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: #008080;">modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modules</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="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="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">reset</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <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="nc" style="color: #458; font-weight: 600;">AnalysisQueue</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">addToQueue</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>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run</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="LC64" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</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="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisStarted</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>
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68
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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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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> </span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqCount</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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72
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<pre style="margin: 0;">-<span id="LC72" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seqCount</span><span class="o" style="font-weight: 600;">;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">;</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="n" style="color: #333;">seq</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="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</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>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisExceptionReceived</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;">e</span><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 class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> </span>
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86
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<pre style="margin: 0;">-<span id="LC86" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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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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<pre style="margin: 0;">-<span id="LC87" 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;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFiltered</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">())</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">processSequence</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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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <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>
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91
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<pre style="margin: 0;">-<span id="LC91" 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;">seqCount</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">1000</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="o" style="font-weight: 600;">{</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPercentComplete</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">percentComplete</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 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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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="n" style="color: #333;">percentComplete</span> <span class="o" style="font-weight: 600;">=</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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPercentComplete</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 class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">;</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> </span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisUpdated</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;">seqCount</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">percentComplete</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Thread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sleep</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">);</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">InterruptedException</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>
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104
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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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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> </span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisComplete</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;">modules</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Analysis</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.BasicStats</span><span class="o" style="font-weight: 600;">;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFormatException</span><span class="o" style="font-weight: 600;">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">AnalysisRunner</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Runnable</span> <span class="o" style="font-weight: 600;">{</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</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="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">listeners</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span><span class="o" style="font-weight: 600;">>();</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" 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;">percentComplete</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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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">AnalysisRunner</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" 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: #008080;">file</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>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addAnalysisListener</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" 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;">l</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="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">removeAnalysisListener</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" 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;">l</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;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">);</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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53
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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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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> </span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">startAnalysis</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" 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: #008080;">modules</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">reset</span><span class="o" style="font-weight: 600;">();</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AnalysisQueue</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">addToQueue</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>
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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>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"></span>
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64
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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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</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="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisStarted</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>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> </span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqCount</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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73
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<pre style="margin: 0;">+<span id="LC73" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">seqCount</span><span class="o" style="font-weight: 600;">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">seq</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="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</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>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisExceptionReceived</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;">e</span><span class="o" style="font-weight: 600;">);</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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85
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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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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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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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<pre style="margin: 0;">+<span id="LC88" 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;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFiltered</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">())</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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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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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">processSequence</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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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> </span>
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<td class="diff-line-num new old_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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<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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<pre style="margin: 0;">+<span id="LC92" 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;">seqCount</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">1000</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="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPercentComplete</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">percentComplete</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 class="o" style="font-weight: 600;">{</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="n" style="color: #333;">percentComplete</span> <span class="o" style="font-weight: 600;">=</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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getPercentComplete</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 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 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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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC98" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisUpdated</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;">seqCount</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">percentComplete</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Thread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sleep</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">);</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">InterruptedException</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>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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107
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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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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We need to account for their potentially being no sequences</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// in the file. In this case the BasicStats module never gets </span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the file name so we need to explicitly pass it.</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" 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;">seqCount</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="o" style="font-weight: 600;">{</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" 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;">modules</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="k" style="font-weight: 600;">instanceof</span> <span class="nc" style="color: #458; font-weight: 600;">BasicStats</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">BasicStats</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">modules</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="na" style="color: #008080;">setFileName</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">listeners</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" 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;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">analysisComplete</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;">modules</span><span class="o" style="font-weight: 600;">);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> </span>
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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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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#84fff692b48938cf047014dc655e47eccf9f4c11"><strong>uk/ac/babraham/FastQC/Analysis/OfflineRunner.java</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Analysis</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.atomic.AtomicInteger</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.FastQCConfig</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.ModuleFactory</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFactory</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
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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;">uk.ac.babraham.FastQC.Utilities.CasavaBasename</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;">uk.ac.babraham.FastQC.Utilities.NanoporeBasename</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>
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<pre style="margin: 0;">-<span id="LC36" 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;">OfflineRunner</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</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>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span> <span class="n" style="color: #333;">filesRemaining</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="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">showUpdates</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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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">OfflineRunner</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">filenames</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="LC42" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we need to show updates</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="n" style="color: #333;">showUpdates</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">quiet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We make a special case if they supply a single filename</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// which is stdin. In this case we'll take data piped to us</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// rather than trying to read the actual file. We'll also</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// skip the existence check.</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC53" 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;">filenames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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;">filenames</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: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin"</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="LC54" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filenames</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="LC55" class="line" lang="java"> <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="k" style="font-weight: 600;">else</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="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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC60" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</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="na" style="color: #008080;">canRead</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="LC61" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Skipping '"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">"' which didn't exist, or couldn't be read"</span><span class="o" style="font-weight: 600;">);</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</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="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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nano</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="na" style="color: #008080;">isDirectory</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fast5files</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="na" style="color: #008080;">listFiles</span><span class="o" style="font-weight: 600;">();</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" 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="n" style="color: #333;">fast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" 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;">fast5files</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="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">endsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fast5"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fast5files</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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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// In newer nanopore software instances the fast5 files are</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// put into subdirectories of the main one specified so we</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// also need to look into those as well.</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" 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="n" style="color: #333;">fast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" 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;">fast5files</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="na" style="color: #008080;">isDirectory</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">subFast5files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5files</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="na" style="color: #008080;">listFiles</span><span class="o" style="font-weight: 600;">();</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> </span>
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80
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<pre style="margin: 0;">-<span id="LC80" 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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">subFast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" 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;">subFast5files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">endsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fast5"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subFast5files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <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;">else</span> <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="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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>
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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 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="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>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">fileGroups</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>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we need to group together files from a casava group</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">casava</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="LC101" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">CasavaBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCasavaGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <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;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nano</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="LC104" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">NanoporeBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNanoporeGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</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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108
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<pre style="margin: 0;">-<span id="LC108" 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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">elementAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> </span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">somethingFailed</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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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> </span>
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118
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<pre style="margin: 0;">-<span id="LC118" 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="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"></span>
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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>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">processFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileGroups</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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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fileGroups</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>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="n" style="color: #333;">somethingFailed</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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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> </span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We need to hold this class open as otherwise the main method</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// exits when it's finished.</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" 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;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Thread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sleep</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">InterruptedException</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>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC139" 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;">somethingFailed</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</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="LC143" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> </span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processFile</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC147" 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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC148" 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;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" 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;">IOException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">" doesn't exist"</span><span class="o" style="font-weight: 600;">);</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequenceFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">);</span> </span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> </span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AnalysisRunner</span> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AnalysisRunner</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">);</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAnalysisListener</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>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> </span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">module_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getStandardModuleList</span><span class="o" style="font-weight: 600;">();</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startAnalysis</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">module_list</span><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="LC161" class="line" lang="java"> <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>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisComplete</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">reportFile</span><span class="o" style="font-weight: 600;">;</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> </span>
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166
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<pre style="margin: 0;">-<span id="LC166" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Analysis complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">output_dir</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>
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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fileName</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="na" style="color: #008080;">getFile</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.gz$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bz2$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.txt$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fq$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.csfastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.sam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"_fastqc.html"</span><span class="o" style="font-weight: 600;">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">reportFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">output_dir</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;">fileName</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<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 old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="n" style="color: #333;">reportFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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="na" style="color: #008080;">getFile</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAbsolutePath</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.gz$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bz2$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.txt$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fq$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.csfastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.sam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"_fastqc.html"</span><span class="o" style="font-weight: 600;">);</span> </span>
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175
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<pre style="margin: 0;">-<span id="LC175" 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="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> </span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">HTMLReportArchive</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;">results</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reportFile</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" 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="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">analysisExceptionReceived</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;">e</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><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">
183
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<pre style="margin: 0;">-<span id="LC183" 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="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</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>
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186
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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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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisUpdated</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</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;">sequencesProcessed</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;">percentComplete</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> </span>
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190
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<pre style="margin: 0;">-<span id="LC190" 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;">percentComplete</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" 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;">percentComplete</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">105</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"It seems our guess for the total number of records wasn't very good. Sorry about that."</span><span class="o" style="font-weight: 600;">);</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" 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;">percentComplete</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Still going at "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"% complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Approx "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"% complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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201
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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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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisExceptionReceived</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process file "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</span><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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisStarted</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Started analysis of "</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="na" style="color: #008080;">name</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>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> <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>
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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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<pre style="margin: 0;">+<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Analysis</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.atomic.AtomicInteger</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.FastQCConfig</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.ModuleFactory</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Modules.QCModule</span><span class="o" style="font-weight: 600;">;</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFactory</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Sequence.SequenceFile</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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33
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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;">uk.ac.babraham.FastQC.Utilities.CasavaBasename</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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34
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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;">uk.ac.babraham.FastQC.Utilities.NanoporeBasename</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" 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;">OfflineRunner</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">AnalysisListener</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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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="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span> <span class="n" style="color: #333;">filesRemaining</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="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">showUpdates</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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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">OfflineRunner</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">filenames</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="LC42" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we need to show updates</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="n" style="color: #333;">showUpdates</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">quiet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>();</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We make a special case if they supply a single filename</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// which is stdin. In this case we'll take data piped to us</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// rather than trying to read the actual file. We'll also</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// skip the existence check.</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC53" 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;">filenames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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;">filenames</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: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin"</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="LC54" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filenames</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="LC55" class="line" lang="java"> <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="k" style="font-weight: 600;">else</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="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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</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="na" style="color: #008080;">canRead</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Skipping '"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]+</span><span class="s" style="color: #d14;">"' which didn't exist, or couldn't be read"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nano</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="na" style="color: #008080;">isDirectory</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fast5files</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="na" style="color: #008080;">listFiles</span><span class="o" style="font-weight: 600;">();</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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="n" style="color: #333;">fast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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;">fast5files</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="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">endsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fast5"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fast5files</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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// In newer nanopore software instances the fast5 files are</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// put into subdirectories of the main one specified so we</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// also need to look into those as well.</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" 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="n" style="color: #333;">fast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" 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;">fast5files</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="na" style="color: #008080;">isDirectory</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">subFast5files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5files</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="na" style="color: #008080;">listFiles</span><span class="o" style="font-weight: 600;">();</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" 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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">subFast5files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">subFast5files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">endsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fast5"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subFast5files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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>
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92
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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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93
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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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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we need to group together files from a casava group</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">casava</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">CasavaBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCasavaGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nano</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">NanoporeBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNanoporeGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</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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108
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<pre style="margin: 0;">+<span id="LC108" 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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">elementAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> </span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">somethingFailed</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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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> </span>
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118
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<pre style="margin: 0;">+<span id="LC118" 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="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"></span>
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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>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">processFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileGroups</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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">OutOfMemoryError</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>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Ran out of memory for "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fileGroups</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>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</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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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fileGroups</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>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="n" style="color: #333;">somethingFailed</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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133
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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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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We need to hold this class open as otherwise the main method</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// exits when it's finished.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" 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;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Thread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sleep</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">InterruptedException</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>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" 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;">somethingFailed</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> </span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processFile</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" 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;">IOException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">" doesn't exist"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">sequenceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequenceFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">);</span> </span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AnalysisRunner</span> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AnalysisRunner</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequenceFile</span><span class="o" style="font-weight: 600;">);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java"> <span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAnalysisListener</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>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">module_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleFactory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getStandardModuleList</span><span class="o" style="font-weight: 600;">();</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java"> <span class="n" style="color: #333;">runner</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startAnalysis</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">module_list</span><span class="o" style="font-weight: 600;">);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"> </span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisComplete</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QCModule</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">reportFile</span><span class="o" style="font-weight: 600;">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Analysis complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> </span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">output_dir</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>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fileName</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="na" style="color: #008080;">getFile</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.gz$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bz2$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.txt$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fq$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.csfastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.sam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"_fastqc.html"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="n" style="color: #333;">reportFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FastQCConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getInstance</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">output_dir</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;">fileName</span><span class="o" style="font-weight: 600;">);</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">reportFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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="na" style="color: #008080;">getFile</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">getAbsolutePath</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.gz$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bz2$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.txt$"</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.fq$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.csfastq$"</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="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.sam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\\.bam$"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)+</span><span class="s" style="color: #d14;">"_fastqc.html"</span><span class="o" style="font-weight: 600;">);</span> </span>
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182
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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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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">HTMLReportArchive</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;">results</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reportFile</span><span class="o" style="font-weight: 600;">);</span></span>
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186
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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 new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="n" style="color: #333;">analysisExceptionReceived</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;">e</span><span class="o" style="font-weight: 600;">);</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</span><span class="o" style="font-weight: 600;">();</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisUpdated</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</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;">sequencesProcessed</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;">percentComplete</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> </span>
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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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<pre style="margin: 0;">+<span id="LC197" 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;">percentComplete</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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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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<pre style="margin: 0;">+<span id="LC198" 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;">percentComplete</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">105</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_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">
199
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<pre style="margin: 0;">+<span id="LC199" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"It seems our guess for the total number of records wasn't very good. Sorry about that."</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" 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;">percentComplete</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Still going at "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"% complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Approx "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">percentComplete</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"% complete for "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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206
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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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</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">
208
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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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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"></span>
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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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisExceptionReceived</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Exception</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>
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<td class="diff-line-num new new_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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Failed to process file "</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java"> <span class="n" style="color: #333;">filesRemaining</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">decrementAndGet</span><span class="o" style="font-weight: 600;">();</span></span>
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214
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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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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">analysisStarted</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
</pre>
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217
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<pre style="margin: 0;">+<span id="LC217" 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;">showUpdates</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Started analysis of "</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="na" style="color: #008080;">name</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>
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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="LC220" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="4abecb201fc238d51df86967669e9721b0b19f86">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#4abecb201fc238d51df86967669e9721b0b19f86"><strong>uk/ac/babraham/FastQC/FastQCApplication.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">@@ -54,7 +54,7 @@ import uk.ac.babraham.FastQC.Utilities.NanoporeBasename;</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC55" 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;">FastQCApplication</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">JFrame</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>
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<pre style="margin: 0;">-<span id="LC57" 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="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.<span class="idiff left right">8</span>"</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;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.<span class="idiff left right">9</span>"</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>
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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="nc" style="color: #458; font-weight: 600;">JTabbedPane</span> <span class="n" style="color: #333;">fileTabs</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="nc" style="color: #458; font-weight: 600;">WelcomePanel</span> <span class="n" style="color: #333;">welcomePanel</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">@@ -318,8 +318,14 @@ public class FastQCApplication extends JFrame {</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Recent java themes for linux are just horribly broken with missing</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// bits of UI. We're therefore not going to set a native look if</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we're on linux. See seqmonk bug #95 for details.</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setLookAndFeel</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSystemLookAndFeelClassName</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getProperty</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"os.name"</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">toLowerCase</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"linux"</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="LC327" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setLookAndFeel</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">UIManager</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSystemLookAndFeelClassName</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC329" 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="nc" style="color: #458; font-weight: 600;">Exception</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>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"> </span>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#e9f63f51554c886d766c4f8514ac17292120173c"><strong>uk/ac/babraham/FastQC/Graphs/LineGraph.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,7 +139,7 @@ public class LineGraph extends JPanel {</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java"> </span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now draw the data points</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">))/</span><span class="n" style="color: #333;"><span class="idiff left">data</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">length</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="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">baseWidth</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getWidth</span><span class="o" style="font-weight: 600;">()-(</span><span class="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">))/</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Math</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">max</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="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// Math.max is there in case we have no data (no sequences)</span></span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" 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;">baseWidth</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;">baseWidth</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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144
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"> </span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// System.out.println("Base Width is "+baseWidth);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -183,8 +183,9 @@ public class LineGraph extends JPanel {</td>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> </span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" 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;">d</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;">d</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: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setColor</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">COLOURS</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="no" style="color: #008080;">COLOURS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</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="n" style="color: #333;">d</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="LC186" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC187" 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;">data</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="na" style="color: #008080;">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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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="n" style="color: #333;">lastY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</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="n" style="color: #333;">d</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="LC189" 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;">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="n" style="color: #333;">data</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="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisY</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getY</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="n" style="color: #333;">d</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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190
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">drawLine</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">baseWidth</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="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</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;">1</span><span class="o" style="font-weight: 600;">)),</span> <span class="n" style="color: #333;">lastY</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseWidth</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="n" style="color: #333;">xOffset</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">baseWidth</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="n" style="color: #333;">thisY</span><span class="o" style="font-weight: 600;">);</span></span>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#46343b9eab75ba9806dd1e6132091498ce2ff3bf"><strong>uk/ac/babraham/FastQC/Modules/AdapterContent.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">@@ -146,10 +146,13 @@ public class AdapterContent extends AbstractQCModule {</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// than we've seen before, but also that the last position we could find a hit</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// is a positive position.</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If the sequence is longer than it was then we need to expand the storage in</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// all of the adapter objects to account for this.</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC152" 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;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequence</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">longestSequence</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequence</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">longestAdapter</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">longestSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequence</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC154" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">adapters</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="n" style="color: #333;">adapters</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">expandLengthTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">longestSequence</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">longestAdapter</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">adapters</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">expandLengthTo</span><span class="o" style="font-weight: 600;">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">longestSequence</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">longestAdapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC158" 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">@@ -311,9 +314,10 @@ public class AdapterContent extends AbstractQCModule {</td>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">incrementCount</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;">position</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="LC316" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC314" 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;">position</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">positions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="LC315" class="line" lang="java"> <span class="n" style="color: #333;">expandLengthTo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">position</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="LC316" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Don't ever check or expand the storage within this</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// function as it ends up double counting previously</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// incremented positions. Rely on the upstream code</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// having done the expansion correctly already.</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">positions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">];</span> </span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="java"></span>
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<li id="2f80f99e3f19d949f693ab40702d4730e21cd809">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#2f80f99e3f19d949f693ab40702d4730e21cd809"><strong>uk/ac/babraham/FastQC/Modules/BasicStats.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">@@ -83,12 +83,16 @@ public class BasicStats extends AbstractQCModule {</td>
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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="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</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="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Basic Statistics"</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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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setFileName</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</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="LC88" 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: #008080;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> </span>
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<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: #008080;">name</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: #008080;">name</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceFirst</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="LC91" class="line" lang="java"> <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="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">sequence</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="LC94" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC89" 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;">name</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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">name</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>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceFirst</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"stdin:"</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="LC95" 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;">name</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;">setFileName</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">name</span><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>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If this is a filtered sequence we simply count it and move on.</span></span>
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<pre style="margin: 0;"> <span id="LC98" 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;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFiltered</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<li id="599886f55ff6b2afb619da338a48b076cd60db4b">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#599886f55ff6b2afb619da338a48b076cd60db4b"><strong>uk/ac/babraham/FastQC/Modules/DuplicationLevel.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">@@ -151,6 +151,7 @@ public class DuplicationLevel extends AbstractQCModule {</td>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dedupTotal</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rawTotal</span><span class="o" style="font-weight: 600;">)*</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC154" 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;">rawTotal</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;">percentDifferentSeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> </span>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#ff73039d6f80221ab4399063f3ba9f2bc2a7017a"><strong>uk/ac/babraham/FastQC/Modules/PerTileQualityScores.java</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Modules</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.BaseGroup</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.TileGraph</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span>
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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;">uk.ac.babraham.FastQC.Sequence.Sequence</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;">uk.ac.babraham.FastQC.Sequence.QualityEncoding.PhredEncoding</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;">uk.ac.babraham.FastQC.Utilities.QualityCount</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC37" 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;">PerTileQualityScores</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">perTileQualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</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 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;">currentLength</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="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">means</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="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xLabels</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC45" 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;">high</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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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhredEncoding</span> <span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC47" 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;">calculated</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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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> </span>
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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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">totalCount</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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50
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">splitPosition</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>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxDeviation</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="LC54" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC55" 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;">ignoreInReport</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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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</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="LC58" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC59" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</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>
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<pre style="margin: 0;">-<span id="LC61" 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;">TileGraph</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">means</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="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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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" 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;">ignoreInReport</span> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">currentLength</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="o" style="font-weight: 600;">{</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">getPercentages</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculateOffsets</span><span class="o" style="font-weight: 600;">();</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="n" style="color: #333;">encodingScheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">PhredEncoding</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFastQEncodingOffset</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">high</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offset</span><span class="o" style="font-weight: 600;">();</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" 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;">high</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">35</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">high</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">35</span><span class="o" style="font-weight: 600;">;</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BaseGroup</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">BaseGroup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makeBaseGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentLength</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tileNumbers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</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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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> </span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">);</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> </span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">tiles</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;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" 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="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">tiles</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tileNumbers</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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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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95
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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 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">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">means</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">xLabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"></span>
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99
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<pre style="margin: 0;">-<span id="LC99" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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>
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100
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<pre style="margin: 0;">-<span id="LC100" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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101
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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;">t</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="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">
102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="n" style="color: #333;">xLabels</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"></span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">lowerCount</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">upperCount</span><span class="o" style="font-weight: 600;">();</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getMean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNumbers</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="n" style="color: #333;">minBase</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxBase</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offset</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we normalise across each column to see if there are any tiles with unusually</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// high or low quality.</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxDeviation</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="LC114" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">averageQualitiesPerGroup</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC117" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span> </span>
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<pre style="margin: 0;">-<span id="LC118" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">averageQualitiesPerGroup</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC123" 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="n" style="color: #333;">averageQualitiesPerGroup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">averageQualitiesPerGroup</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="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">averageQualitiesPerGroup</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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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">])></span> <span class="n" style="color: #333;">maxDeviation</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">maxDeviation</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> </span>
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136
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<pre style="margin: 0;">-<span id="LC136" 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: #008080;">maxDeviation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDeviation</span><span class="o" style="font-weight: 600;">;</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"></span>
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140
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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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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">calculateOffsets</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Works out from the set of chars what is the most</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// likely encoding scale for this file.</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">minChar</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="LC147" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">maxChar</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="LC148" class="line" lang="java"></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Use the data from the first tile</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</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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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC152" 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;">q</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;">q</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" 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;">q</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="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">minChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">();</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">maxChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><span class="o" style="font-weight: 600;">();</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minChar</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">minChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">();</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxChar</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="LC162" class="line" lang="java"> <span class="n" style="color: #333;">maxChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">minChar</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxChar</span><span class="o" style="font-weight: 600;">};</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Check if we can skip counting because the module is being ignored anyway</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" 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;">totalCount</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="o" style="font-weight: 600;">{</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> </span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Don't waste time calculating this if we're not going to use it anyway</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" 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;">ignoreInReport</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> </span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Try to find the tile id. This can come in one of two forms:</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// @HWI-1KL136:211:D1LGAACXX:1:1101:18518:48851 3:N:0:ATGTCA</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// ^</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// @HWUSI-EAS493_0001:2:1:1000:16900#0/1</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// ^</span></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// These would appear at sections 2 or 3 of an array split on :</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// This module does quite a lot of work and ends up being the limiting</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// step when calculating. We'll therefore take only a sample of the </span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// sequences to try to get a representative selection.</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> </span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">;</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" 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;">totalCount</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</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="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> </span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First try to split the id by :</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tile</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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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> </span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">splitID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getID</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">split</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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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If there are 7 or more fields then it's a 1.8+ file</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java"> </span>
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210
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<pre style="margin: 0;">-<span id="LC210" 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;">splitPosition</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="o" style="font-weight: 600;">{</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We've found a split position before so let's try to use it again</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> </span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC214" 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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">splitPosition</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="LC215" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// There isn't enough data in this header to split the way we did before</span></span>
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<pre style="margin: 0;">-<span id="LC216" 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;">NumberFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Can't extract a number - not enough data"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">splitPosition</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="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="k" style="font-weight: 600;">else</span> <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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">splitPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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 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;">splitPosition</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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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We can try the older format</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</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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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We're not going to get a tile out of this</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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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234
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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="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="java"> </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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<pre style="margin: 0;">-<span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">nfe</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="LC240" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// This doesn't conform</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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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<pre style="margin: 0;">-<span id="LC242" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getQualityString</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toCharArray</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;">currentLength</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="LC247" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">iterator</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;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</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="LC250" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisTile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</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>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisTile</span><span class="o" style="font-weight: 600;">);</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCountsNew</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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>
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<pre style="margin: 0;">-<span id="LC255" 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="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="java"> <span class="n" style="color: #333;">qualityCountsNew</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</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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<pre style="margin: 0;">-<span id="LC257" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="n" style="color: #333;">qualityCountsNew</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="java"> <span class="n" style="color: #333;">qualityCountsNew</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="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">();</span> </span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisTile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qualityCountsNew</span><span class="o" style="font-weight: 600;">);</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="java"></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="java"> <span class="n" style="color: #333;">currentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="java"></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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268
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<pre style="margin: 0;">-<span id="LC268" 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;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="java"> </span>
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270
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<pre style="margin: 0;">-<span id="LC270" 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;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// There are too many tiles, so we're probably parsing this wrong.</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Let's give up</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Too many tiles (>1000) so giving up trying to do per-tile qualities since we're probably parsing the file wrongly"</span><span class="o" style="font-weight: 600;">);</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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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<pre style="margin: 0;">-<span id="LC275" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">currentLength</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC280" 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="n" style="color: #333;">currentLength</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="java"> <span class="n" style="color: #333;">qualityCounts</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="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC289" 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="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="java"> <span class="n" style="color: #333;">qualityCounts</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="na" style="color: #008080;">addValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">qual</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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<pre style="margin: 0;">-<span id="LC291" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="java"></span>
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<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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</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="LC296" class="line" lang="java"> <span class="n" style="color: #333;">totalCount</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="LC297" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[]>();</span></span>
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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;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Shows the perl tile Quality scores of all bases at a given position in a sequencing run"</span><span class="o" style="font-weight: 600;">;</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="java"></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Per tile sequence quality"</span><span class="o" style="font-weight: 600;">;</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="java"></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="java"></span>
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311
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<pre style="margin: 0;">-<span id="LC311" 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;">maxDeviation</span> <span class="o" style="font-weight: 600;">></span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="java"></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="java"> </span>
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318
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<pre style="margin: 0;">-<span id="LC318" 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;">maxDeviation</span> <span class="o" style="font-weight: 600;">></span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC323" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="java"> </span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"per_tile_quality.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Per <span class="idiff left">base quality graph"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Math</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">max</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">800</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">xLabels</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">15</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">600</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="LC326" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Tile\tBase\tMean\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC330" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC331" 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="n" style="color: #333;">means</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: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tiles</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>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabels</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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<pre style="margin: 0;">-<span id="LC337" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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>
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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="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getMean</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;">tile</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;">minbp</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;">maxbp</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="java"> <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 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="LC348" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">total</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="LC349" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC352" 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;">minbp</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="n" style="color: #333;">maxbp</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC353" 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;">qualityCounts</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="na" style="color: #008080;">getTotalCount</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="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="LC354" class="line" lang="java"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="java"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">qualityCounts</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="na" style="color: #008080;">getMean</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="LC356" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC359" 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;">count</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">total</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>
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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;">return</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="LC363" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span><span class="idiff left right">
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span><span class="idiff left right">
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span><span class="idiff left right">
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span><span class="idiff left right">
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span><span class="idiff left right">
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span><span class="idiff left right">
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span><span class="idiff left right">
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span><span class="idiff left right">
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span><span class="idiff left right">
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span><span class="idiff left right">
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span><span class="idiff left right">
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span><span class="idiff left right">
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span><span class="idiff left right">
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span><span class="idiff left right">
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Modules</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC24" 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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Iterator</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.swing.JPanel</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">javax.xml.stream.XMLStreamException</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.BaseGroup</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Graphs.TileGraph</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">uk.ac.babraham.FastQC.Report.HTMLReportArchive</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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33
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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;">uk.ac.babraham.FastQC.Sequence.Sequence</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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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;">uk.ac.babraham.FastQC.Sequence.QualityEncoding.PhredEncoding</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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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;">uk.ac.babraham.FastQC.Utilities.QualityCount</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" 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;">PerTileQualityScores</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">AbstractQCModule</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">perTileQualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[]>();</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC41" 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;">currentLength</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><span class="idiff left right">
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">means</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><span class="idiff left right">
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">xLabels</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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44
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<pre style="margin: 0;">+<span id="LC44" 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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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45
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<pre style="margin: 0;">+<span id="LC45" 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;">high</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><span class="idiff left right">
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhredEncoding</span> <span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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47
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<pre style="margin: 0;">+<span id="LC47" 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;">calculated</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><span class="idiff left right">
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> </span><span class="idiff left right">
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49
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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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">totalCount</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><span class="idiff left right">
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> </span><span class="idiff left right">
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51
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">splitPosition</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><span class="idiff left right">
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> </span><span class="idiff left right">
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxDeviation</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><span class="idiff left right">
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" 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;">ignoreInReport</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><span class="idiff left right">
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">JPanel</span> <span class="nf" style="color: #900; font-weight: 600;">getResultsPanel</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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;">TileGraph</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabels</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">means</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreFilteredSequences</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreInReport</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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70
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<pre style="margin: 0;">+<span id="LC70" 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;">ignoreInReport</span> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">currentLength</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">synchronized</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">getPercentages</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"></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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculateOffsets</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="n" style="color: #333;">encodingScheme</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">PhredEncoding</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFastQEncodingOffset</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">high</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offset</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" 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;">high</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">35</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="n" style="color: #333;">high</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">35</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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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="nc" style="color: #458; font-weight: 600;">BaseGroup</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">BaseGroup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makeBaseGroups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentLength</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Integer</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tileNumbers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> </span><span class="idiff left right">
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="n" style="color: #333;">tiles</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;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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92
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<pre style="margin: 0;">+<span id="LC92" 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="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="n" style="color: #333;">tiles</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tileNumbers</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> </span><span class="idiff left right">
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">means</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">xLabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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><span class="idiff left right">
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100
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<pre style="margin: 0;">+<span id="LC100" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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101
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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;">t</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><span class="idiff left right">
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="n" style="color: #333;">xLabels</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">lowerCount</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</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="na" style="color: #008080;">upperCount</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getMean</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNumbers</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="n" style="color: #333;">minBase</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxBase</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">encodingScheme</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offset</span><span class="o" style="font-weight: 600;">());</span></span><span class="idiff left right">
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> </span><span class="idiff left right">
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Now we normalise across each column to see if there are any tiles with unusually</span></span><span class="idiff left right">
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// high or low quality.</span></span><span class="idiff left right">
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> </span><span class="idiff left right">
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxDeviation</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><span class="idiff left right">
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> </span><span class="idiff left right">
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">averageQualitiesPerGroup</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> </span><span class="idiff left right">
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117
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<pre style="margin: 0;">+<span id="LC117" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span> </span><span class="idiff left right">
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118
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<pre style="margin: 0;">+<span id="LC118" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">averageQualitiesPerGroup</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="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> </span><span class="idiff left right">
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123
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<pre style="margin: 0;">+<span id="LC123" 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="n" style="color: #333;">averageQualitiesPerGroup</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">averageQualitiesPerGroup</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="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" 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="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tileNumbers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">averageQualitiesPerGroup</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><span class="idiff left right">
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">])></span> <span class="n" style="color: #333;">maxDeviation</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="n" style="color: #333;">maxDeviation</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> </span><span class="idiff left right">
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136
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<pre style="margin: 0;">+<span id="LC136" 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: #008080;">maxDeviation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxDeviation</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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><span class="idiff left right">
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">calculateOffsets</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Works out from the set of chars what is the most</span></span><span class="idiff left right">
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// likely encoding scale for this file.</span></span><span class="idiff left right">
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">minChar</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><span class="idiff left right">
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">maxChar</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><span class="idiff left right">
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Use the data from the first tile</span></span><span class="idiff left right">
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</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><span class="idiff left right">
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" 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;">q</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;">q</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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153
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<pre style="margin: 0;">+<span id="LC153" 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;">q</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">minChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">maxChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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158
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<pre style="margin: 0;">+<span id="LC158" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minChar</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">minChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMinChar</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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161
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<pre style="margin: 0;">+<span id="LC161" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxChar</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java"> <span class="n" style="color: #333;">maxChar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getMaxChar</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">minChar</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">maxChar</span><span class="o" style="font-weight: 600;">};</span></span><span class="idiff left right">
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSequence</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Check if we can skip counting because the module is being ignored anyway</span></span><span class="idiff left right">
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173
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<pre style="margin: 0;">+<span id="LC173" 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;">totalCount</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"ignore"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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><span class="idiff left right">
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Don't waste time calculating this if we're not going to use it anyway</span></span><span class="idiff left right">
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181
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<pre style="margin: 0;">+<span id="LC181" 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;">ignoreInReport</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> </span><span class="idiff left right">
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <span class="n" style="color: #333;">calculated</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><span class="idiff left right">
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Try to find the tile id. This can come in one of two forms:</span></span><span class="idiff left right">
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// @HWI-1KL136:211:D1LGAACXX:1:1101:18518:48851 3:N:0:ATGTCA</span></span><span class="idiff left right">
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// ^</span></span><span class="idiff left right">
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// @HWUSI-EAS493_0001:2:1:1000:16900#0/1</span></span><span class="idiff left right">
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// ^</span></span><span class="idiff left right">
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// These would appear at sections 2 or 3 of an array split on :</span></span><span class="idiff left right">
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// This module does quite a lot of work and ends up being the limiting</span></span><span class="idiff left right">
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// step when calculating. We'll therefore take only a sample of the </span></span><span class="idiff left right">
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// sequences to try to get a representative selection.</span></span><span class="idiff left right">
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> </span><span class="idiff left right">
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">totalCount</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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198
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<pre style="margin: 0;">+<span id="LC198" 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;">totalCount</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10</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="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="java"> </span><span class="idiff left right">
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// First try to split the id by :</span></span><span class="idiff left right">
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tile</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><span class="idiff left right">
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"> </span><span class="idiff left right">
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">splitID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getID</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">split</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><span class="idiff left right">
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"></span>
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205
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If there are 7 or more fields then it's a 1.8+ file</span></span><span class="idiff left right">
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> </span><span class="idiff left right">
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210
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<pre style="margin: 0;">+<span id="LC210" 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;">splitPosition</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We've found a split position before so let's try to use it again</span></span><span class="idiff left right">
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"> </span><span class="idiff left right">
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java"> </span><span class="idiff left right">
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214
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<pre style="margin: 0;">+<span id="LC214" 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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">splitPosition</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// There isn't enough data in this header to split the way we did before</span></span><span class="idiff left right">
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216
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<pre style="margin: 0;">+<span id="LC216" 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;">NumberFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Can't extract a number - not enough data"</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">splitPosition</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"> </span><span class="idiff left right">
</span></pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">splitPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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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">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <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;">splitID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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 class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java"> <span class="n" style="color: #333;">splitPosition</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><span class="idiff left right">
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We can try the older format</span></span><span class="idiff left right">
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">splitID</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><span class="idiff left right">
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We're not going to get a tile out of this</span></span><span class="idiff left right">
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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><span class="idiff left right">
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234
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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="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java"> </span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java"> </span><span class="idiff left right">
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NumberFormatException</span> <span class="n" style="color: #333;">nfe</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// This doesn't conform</span></span><span class="idiff left right">
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getQualityString</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toCharArray</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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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;">currentLength</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="java"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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249
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<pre style="margin: 0;">+<span id="LC249" 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;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thisTile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="java"></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisTile</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCountsNew</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="java"></span>
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255
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<pre style="margin: 0;">+<span id="LC255" 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="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="java"> <span class="n" style="color: #333;">qualityCountsNew</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualityCounts</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><span class="idiff left right">
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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258
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<pre style="margin: 0;">+<span id="LC258" 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;">qualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="n" style="color: #333;">qualityCountsNew</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="java"> <span class="n" style="color: #333;">qualityCountsNew</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="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">();</span> </span><span class="idiff left right">
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">thisTile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qualityCountsNew</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="java"></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="java"> <span class="n" style="color: #333;">currentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" 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;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="java"> </span><span class="idiff left right">
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270
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<pre style="margin: 0;">+<span id="LC270" 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;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// There are too many tiles, so we're probably parsing this wrong.</span></span><span class="idiff left right">
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Let's give up</span></span><span class="idiff left right">
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Too many tiles (>1000) so giving up trying to do per-tile qualities since we're probably parsing the file wrongly"</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="java"> <span class="n" style="color: #333;">ignoreInReport</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><span class="idiff left right">
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="java"> </span><span class="idiff left right">
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">currentLength</span><span class="o" style="font-weight: 600;">];</span></span><span class="idiff left right">
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280
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<pre style="margin: 0;">+<span id="LC280" 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="n" style="color: #333;">currentLength</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="java"> <span class="n" style="color: #333;">qualityCounts</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="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="java"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qualityCounts</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="java"></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC289" 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="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="java"> <span class="n" style="color: #333;">qualityCounts</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="na" style="color: #008080;">addValue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">qual</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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292
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">reset</span> <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="java"> <span class="n" style="color: #333;">totalCount</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="java"> <span class="n" style="color: #333;">perTileQualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span><span class="o" style="font-weight: 600;">[]>();</span></span><span class="idiff left right">
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">description</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Shows the perl tile Quality scores of all bases at a given position in a sequencing run"</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="java"></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Per tile sequence quality"</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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307
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesError</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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309
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<pre style="margin: 0;">+<span id="LC309" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" 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;">maxDeviation</span> <span class="o" style="font-weight: 600;">></span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"error"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">raisesWarning</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" 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;">maxDeviation</span> <span class="o" style="font-weight: 600;">></span> <span class="nc" style="color: #458; font-weight: 600;">ModuleConfig</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getParam</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tile"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"warn"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="java"></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">makeReport</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">HTMLReportArchive</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">XMLStreamException</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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<pre style="margin: 0;">+<span id="LC323" 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;">calculated</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">getPercentages</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="java"> </span><span class="idiff left right">
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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="java"> <span class="n" style="color: #333;">writeDefaultImage</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"per_tile_quality.png"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Per <span class="idiff left">tile quality graph"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Math</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">max</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">800</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">xLabels</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">length</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">15</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">600</span></span><span class="o" style="font-weight: 600;"><span class="idiff">);</span></span></span><span class="idiff right">
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="java"></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">dataDocument</span><span class="o" style="font-weight: 600;">();</span></span><span class="idiff left right">
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"#Tile\tBase\tMean\n"</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC330" 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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC331" 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="n" style="color: #333;">means</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: #008080;">length</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tiles</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xLabels</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">means</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]);</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">getMean</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;">tile</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;">minbp</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;">maxbp</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="java"> <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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">total</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">QualityCount</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">qualityCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">perTileQualityCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">);</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC352" 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;">minbp</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="n" style="color: #333;">maxbp</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC353" 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;">qualityCounts</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="na" style="color: #008080;">getTotalCount</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="java"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++;</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="java"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">qualityCounts</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="na" style="color: #008080;">getMean</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC359" 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;">count</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="o" style="font-weight: 600;">{</span></span><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">total</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><span class="idiff left right">
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span><span class="idiff left right">
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#c374db931477fae930a0a924ef5dec32c2a7cd32"><strong>uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.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">@@ -68,7 +68,12 @@ public class SequenceLengthDistribution extends AbstractQCModule {</td>
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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="n" style="color: #333;">maxLen</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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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <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>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We can get a -1 value for min if there aren't any valid sequences</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// at all.</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC76" 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;">minLen</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;">minLen</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="LC77" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We put one extra category either side of the actual size</span></span>
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<pre style="margin: 0;"> <span id="LC79" 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;">minLen</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;">minLen</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="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">...</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">@@ -194,9 +199,12 @@ public class SequenceLengthDistribution extends AbstractQCModule {</td>
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194
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC198" 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;">lengthCounts</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</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="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We might not have any sequences so only check if we do</span></span>
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<pre style="margin: 0;">+<span id="LC203" 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;">lengthCounts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Empty sequences get us an error</span></span>
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<pre style="margin: 0;">+<span id="LC205" 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;">lengthCounts</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</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="LC206" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><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 class="o" style="font-weight: 600;">}</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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<pre style="margin: 0;"> <span id="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#3013cb0481f38b744114f30dd2156d353af7ebf7"><strong>uk/ac/babraham/FastQC/Results/ResultsPanel.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">@@ -124,7 +124,7 @@ public class ResultsPanel extends JPanel implements ListSelectionListener, Analy</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">panels</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">JPanel</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> </span>
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126
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<pre style="margin: 0;"> <span id="LC126" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">modules</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Getting panel for "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">modules</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="na" style="color: #008080;">name</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">" with "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">modules</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="na" style="color: #008080;">description</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span> System.err.println("Getting panel for "+modules[m].name()+" with "+modules[m].description());</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="n" style="color: #333;">panels</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modules</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="na" style="color: #008080;">getResultsPanel</span><span class="o" style="font-weight: 600;">();</span></span>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"> </span>
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<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#b814303178e7f8f116f1ffd8cc7f1791e501935b"><strong>uk/ac/babraham/FastQC/Sequence/Fast5File.java</strong></a>
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<pre style="margin: 0;">-<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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<pre style="margin: 0;">-<span id="LC3" 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="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ch.systemsx.cisd.hdf5.HDF5Factory</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ch.systemsx.cisd.hdf5.IHDF5SimpleReader</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC28" 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;">Fast5File</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">nextSequence</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="LC31" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</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>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="nf" style="color: #900; font-weight: 600;">Fast5File</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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: #008080;">file</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>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="n" style="color: #333;">name</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="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IHDF5SimpleReader</span> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">HDF5Factory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">openForReading</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>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rdfPaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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="LC42" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_2D_000/BaseCalled_template/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_2D_000/BaseCalled_2D/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_1D_000/BaseCalled_template/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_1D_000/BaseCalled_1D/Fastq"</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">foundPath</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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<pre style="margin: 0;">-<span id="LC49" 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;">r</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;">r</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rdfPaths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rdfPaths</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="n" style="color: #333;">foundPath</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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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rdfPaths</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>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sections</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</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>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> </span>
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58
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<pre style="margin: 0;">-<span id="LC58" 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;">sections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" 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;">SequenceFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Didn't get 4 sections from "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fastq</span><span class="o" style="font-weight: 600;">);</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> </span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="n" style="color: #333;">nextSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</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;">sections</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="na" style="color: #008080;">toUpperCase</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">sections</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">sections</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="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="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="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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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" 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;">foundPath</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" 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;">SequenceFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No valid fastq paths found in "</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>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <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>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">;</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getPercentComplete</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" 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;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> </span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isColorspace</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">hasNext</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nextSequence</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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91
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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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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"></span>
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93
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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="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</span> <span class="o" style="font-weight: 600;">{</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextSequence</span><span class="o" style="font-weight: 600;">;</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="n" style="color: #333;">nextSequence</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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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">;</span></span>
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97
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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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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"></span>
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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">
99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">remove</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// No action here</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getFile</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">;</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2010-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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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="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<td class="diff-line-num new new_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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Sequence</span><span class="o" style="font-weight: 600;">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" 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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ch.systemsx.cisd.hdf5.HDF5Factory</span><span class="o" style="font-weight: 600;">;</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ch.systemsx.cisd.hdf5.IHDF5SimpleReader</span><span class="o" style="font-weight: 600;">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" 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;">Fast5File</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFile</span> <span class="o" style="font-weight: 600;">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">nextSequence</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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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">;</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">IHDF5SimpleReader</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">readPaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" 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;">readPathsIndexPosition</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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rdfPaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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="LC41" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_2D_000/BaseCalled_template/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_2D_000/BaseCalled_2D/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_1D_000/BaseCalled_template/Fastq"</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="s" style="color: #d14;">"Analyses/Basecall_1D_000/BaseCalled_1D/Fastq"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">protected</span> <span class="nf" style="color: #900; font-weight: 600;">Fast5File</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</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 class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">file</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>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="n" style="color: #333;">name</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="na" style="color: #008080;">getName</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>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">HDF5Factory</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">openForReading</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>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// These files have changed structure over time. Originally they contained</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// a single read per file where the base of the heirarchy was the read </span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// itself.</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Later the files moved to having multiple reads per file. Now there is</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// an additional top level folder per read with the sub-structure being the</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// same as it used to be for the individual reads.</span></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;">//</span></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;">// We need to account for both of these structures.</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>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// See if we can see a bunch of paths starting with "read_" at the top of the</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;">// heirarchy. If we can then we substitute the read paths for these.</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">topLevelFolders</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getGroupMembers</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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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readFolders</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">>();</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">folder</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">topLevelFolders</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Looking at "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" 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;">folder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">startsWith</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"read_"</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">readFolders</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">folder</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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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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79
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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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">readFolders</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We have read folders so we'll replace the default readPaths with</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// the list we made</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="n" style="color: #333;">readPaths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readFolders</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">;</span></span>
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92
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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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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getPercentComplete</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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95
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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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readPathsIndexPosition</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">readPaths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> </span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isColorspace</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">hasNext</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">readPathsIndexPosition</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">readPaths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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104
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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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"></span>
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106
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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="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">SequenceFormatException</span> <span class="o" style="font-weight: 600;">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> </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">
108
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<pre style="margin: 0;">+<span id="LC108" 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;">r</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;">r</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rdfPaths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exists</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readPaths</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">readPathsIndexPosition</span><span class="o" style="font-weight: 600;">]+</span><span class="n" style="color: #333;">rdfPaths</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="o" style="font-weight: 600;">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> </span>
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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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readPaths</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">readPathsIndexPosition</span><span class="o" style="font-weight: 600;">]+</span><span class="n" style="color: #333;">rdfPaths</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>
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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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sections</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</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>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="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;">SequenceFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Didn't get 4 sections from "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fastq</span><span class="o" style="font-weight: 600;">);</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> </span>
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<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="nc" style="color: #458; font-weight: 600;">Sequence</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Sequence</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;">sections</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="na" style="color: #008080;">toUpperCase</span><span class="o" style="font-weight: 600;">(),</span><span class="n" style="color: #333;">sections</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">sections</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 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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">readPathsIndexPosition</span><span class="o" style="font-weight: 600;">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readPathsIndexPosition</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">readPaths</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" 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;">SequenceFormatException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No valid fastq paths found in "</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>
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132
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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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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">remove</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// No action here</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getFile</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">;</span></span>
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140
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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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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="b07e05b73f29161440c9490fa2d0a5ee9e032c8e">
<a href="https://salsa.debian.org/med-team/fastqc/commit/d1c9f051d1e3face771b3d47b0900d1b928c4381#b07e05b73f29161440c9490fa2d0a5ee9e032c8e"><strong>uk/ac/babraham/FastQC/Utilities/NanoporeBasename.java</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2011-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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="LC20" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Utilities</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Hashtable</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC27" 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;">NanoporeBasename</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC29" 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="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This method finds the core name from an ONT fast5 file. It strips off the</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * part which indicates that this file is one of a set and returns the base name with</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * this part removed.</span></span>
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<pre style="margin: 0;">-<span id="LC33" 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="LC34" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * If the filename does not conform to standard CASAVA naming then a NameFormatException</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * is thrown.</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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="LC37" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param originalName</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NameFormatException</span></span>
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<pre style="margin: 0;">-<span id="LC40" 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="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;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getNanoporeBasename</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">originalName</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">NameFormatException</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Files from nanopores look like: Computer_Samplename_number_chXXX_fileXXX_strand.fast5</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We need to reduce this to Computer_Samplename_number</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">subNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">originalName</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">split</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="LC48" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC49" 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;">subNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC50" 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;">NameFormatException</span><span class="o" style="font-weight: 600;">();</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>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subNames</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="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subNames</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="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subNames</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="LC54" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Basename is "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">basename</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>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">basename</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>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">getNanoporeGroups</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">files</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="LC62" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Hashtable</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">fileBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Hashtable</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</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="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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="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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66
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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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"muxscan"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// Control files not containing real data.</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> </span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If a file forms part of a nanopore group then put it into that</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// group.</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">NanoporeBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNanoporeBasename</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">());</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" 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;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>());</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"> <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="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If the file name doesn't appear to be part of a nanopore group</span></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;">// then add it as a singleton</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NameFormatException</span> <span class="n" style="color: #333;">nfe</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="LC83" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"File '"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"' didn't look like part of a CASAVA group"</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="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">newVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>();</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="n" style="color: #333;">newVector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newVector</span><span class="o" style="font-weight: 600;">);</span> </span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC90" 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>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">baseNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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="LC93" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">baseNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="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="n" style="color: #333;">baseNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="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;">fileGroups</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNames</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="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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="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>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">;</span> </span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" 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="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright Copyright 2011-17 Simon Andrews</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of FastQC.</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is free software; you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation; either version 3 of the License, or</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * FastQC is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with FastQC; if not, write to the Free Software</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">uk</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ac</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">babraham</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FastQC</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Utilities</span><span class="o" style="font-weight: 600;">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Hashtable</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Vector</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC27" 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;">NanoporeBasename</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC29" 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="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This method finds the core name from an ONT fast5 file. It strips off the</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * part which indicates that this file is one of a set and returns the base name with</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * this part removed.</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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="LC34" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * If the filename does not conform to standard CASAVA naming then a NameFormatException</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * is thrown.</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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="LC37" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param originalName</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NameFormatException</span></span>
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<pre style="margin: 0;">+<span id="LC40" 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="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;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="nf" style="color: #900; font-weight: 600;">getNanoporeBasename</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">originalName</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">NameFormatException</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Files from nanopores look like: Computer_Samplename_number_chXXX_fileXXX_strand.fast5</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// We need to reduce this to Computer_Samplename_number</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// Some more recent files have names which are just: Computer_Samplename_number.fast5 so </span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// we need to account for those too.</span></span>
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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="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">subNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">originalName</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">replaceAll</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fast5$"</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="na" style="color: #008080;">split</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="LC51" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC52" 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;">subNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</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="LC53" 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;">NameFormatException</span><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="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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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subNames</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="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subNames</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="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subNames</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="LC57" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Basename is "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">basename</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">basename</span><span class="o" style="font-weight: 600;">;</span></span>
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61
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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="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="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">getNanoporeGroups</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">files</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="LC65" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Hashtable</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">fileBases</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Hashtable</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>>();</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="java"> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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;">f</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;">f</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> </span>
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70
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<pre style="margin: 0;">+<span id="LC70" 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;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"muxscan"</span><span class="o" style="font-weight: 600;">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// Control files not containing real data.</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> </span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// If a file forms part of a nanopore group then put it into that</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// group.</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">baseName</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">NanoporeBasename</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getNanoporeBasename</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">());</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" 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;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">,</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>());</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseName</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"></span>
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81
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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="c1" style="color: #998; font-style: italic;">// If the file name doesn't appear to be part of a nanopore group</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// then add it as a singleton</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">NameFormatException</span> <span class="n" style="color: #333;">nfe</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> </span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"File '"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">()+</span><span class="s" style="color: #d14;">"' didn't look like part of a CASAVA group"</span><span class="o" style="font-weight: 600;">);</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">newVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Vector</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">>();</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="java"> <span class="n" style="color: #333;">newVector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">]);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">getName</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">newVector</span><span class="o" style="font-weight: 600;">);</span> </span>
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91
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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="LC92" class="line" lang="java"> </span>
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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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94
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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="nc" style="color: #458; font-weight: 600;">String</span> <span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">baseNames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">fileGroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">baseNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">][];</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" 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="n" style="color: #333;">baseNames</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</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="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">fileGroups</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileBases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseNames</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="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</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="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> </span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fileGroups</span><span class="o" style="font-weight: 600;">;</span> </span>
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104
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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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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